Firstly, we should point out that, as per New Atheist “reasoning,” the primary point to make is that the Flying Spaghetti Monster is not a real alternative at all because it raises an even bigger problem than it solves namely: who spaghettied the spaghetti? We may likewise ask: who amassed the meatballs?
Since we cannot answer these questions the Spaghettied One does not answer anything.
Your word order is misleading, here. You could say that "The primary point I want to make is that, per New Atheist 'reasoning', the FSM is not a real alternative because...". Your current word order, however, indicates that you think that "according to New Atheists, the primary point of the FSM is that it is not a real alternative because...". Unless you are actually starting the article off on the terrible foot of committing the transgression that you accused many atheists of doing earlier (not knowing what you're attacking), this latter version is inappropriate.
As best I can tell, the primary point of the FSM is to hold unsound religious (and, particularly, various Christian) arguments up to the light after stripping away the centuries of tradition and taboo. And, insofar as there are some, reveal sound religious arguments to be worthwhile despite the dubious company they keep. This point is largely achieved at the tips of two lemmas: First, by repeating the essence of an argument with only superficial elements altered, the invalid conclusion becomes more obviously invalid, so the flaws in the argument are more visible. Second, when anti-FSM people (atheist and non-atheist alike) attack the FSM position, the essence of the attack can be repeated, with only the superficial elements changed back, in order to make an equally valid (or invalid) attack on the original argument.
For example,
Christians argue that Christian creationism should be given 'equal time' in the classroom.
Pastafarians argue, mutatis mutandis, that FSM creationism should be given 'equal time' too.
Everyone sane realizes that the Pastafarian argument is bupkis.
Sufficiently many people realize that the Christian argument, which is in essence the exact same argument, is insufficient.
For another example...
A Christian says:
The Flying Spaghetti Monster has a physical body and thus, is not immaterial nor spirit: it has extension in space is therefore limited by spatial dimensions and restricted by locality and thus, is not omnipresent. One adherent of the cult of the Flying Spaghetti Monster made specific reference to its “noodly appendage.”
A Pasfatarian replies:
That's a good point! And, come to think of it, your god had a physical body (Jesus) and thus, was not immaterial nor spirit: he had extension in space was therefore limited by spatial dimensions and restricted by locality and thus, was not omnipresent. At least one adherent of the cult of your god made specific reference to the "hand of God". Gosh, I guess you're right, and neither the FSM nor your god could be the creator revealed by natural revelation!
For another example...
A Christian says:
Since the Flying Spaghetti Monster is physical it is subject to the absorption and deflection of light particles and is therefore visible and particularly hued. Bobby Henderson did claim that the Flying Spaghetti Monster is “invisible and can pass through normal matter” and so either Bobby Henderson is a false prophet or the Flying Spaghetti Monster knows how to traverse dimensions.
A Pastafarian replies:
Oooh, another zinger! And it hits both of us, again! Since Jesus is physical he's subject to the absorption and deflection of light particles and is therefore visible and particularly hued. But the Bible does claim that your god is invisible, "eternal, immortal, invisible" (1 Timothy 1:17) and so either the Bible is a false holy book or your god knows how to traverse dimensions.
For another example...
A Christian says:
Since the Flying Spaghetti Monster’s physical body consists of spaghetti and meatballs the constituents of the godhead are as follows: eggs, salt and pepper, flour, water, beef and or pork, basil, parsley, mushrooms, bread crumbs, oil, etc.
Since these physical entities must have, by necessity, preexisted the Flying Spaghetti Monster it cannot be the uncaused first cause. Moreover, the constituents of spaghetti and meatballs must have been amassed by an Intelligent Chef who not only had access to various physical ingredients and knew how to put them together just right, fine tuned them, but utilized cookware and some form of energy with which to cook the ingredients.
The Flying Spaghetti Monster is made of the very materials which it is alleged to have created. It could not have created itself since it would have to have been in order to have created itself.
Since the Flying Spaghetti Monster is composed of various complex parts that were merged it had a beginning.
Since it is physical it is not immaterial.
Since it had a beginning it had a cause.
Since it had a beginning it is not eternal.
It experiences time and is not eternal.
It is limited by space. This is true even if it can pass though matter since it has to “pass through” it in order to make its way to another location. Therefore, it is not omnipresent.
Since it is composed of material objects it is not a contingent being.
The Flying Spaghetti Monster does not pass the test of natural theology.
A Pastafarian replies:
Darn. Totally ridiculous. You're right. Moreover, since your god's physical body consisted of flesh and bone the constituents of the godhead are as follows: calcium, protein, hemoglobin, water, etc. Since these physical entities must have, by necessity, preexisted your god it cannot be the uncaused first cause. Moreover, the constituents of flesh and bone must have been amassed by an Intelligent Biotechnician who not only had access to various physical ingredients and knew how to put them together just right, fine tuned them, but utilized labware and some form of energy with which to compose the ingredients.
Your god is made of the very materials which it is alleged to have created. It could not have created itself since it would have to have been in order to have created itself.
Since your god is composed of various complex parts that were merged it had a beginning.
Since it is physical it is not immaterial.
Since it had a beginning it had a cause.
Since it had a beginning it is not eternal.
It experiences time and is not eternal.
It is limited by space. This is true even if Jesus could walk on water since he has to “walk on” it in order to make its way to another location. Therefore, it is not omnipresent.
Since it is composed of material objects it is not a contingent being.
Your god does not pass the test of natural theology.
Could you easily pick out the flaws in the Pasafarian's replies? I hope so, since I think even I could... though I might not be able to do so while sticking to any sort of commonly-held Christian theology. I could say that Jesus isn't God, for example, thus cutting off the physicality problems altogether. I could say that God can execute miracles such as being immortal invisible and immaterial yet also being incarnated as a visibly physical mortal, with a cherry and being multiple persons at the same time on top. I'm sure you could come up with much more elegant justifications why your argument doesn't apply to your god but does apply to the FSM.
But unless you were basing your arguments on more than things that don't boil down to "Yeah, but MY god can do and be anything I want him to be!" the Pastafarian can then throw your illogic back in your face. The FSM's body is not the FSM, simply its body, and anyhow the FSM can execute miracles such as being immaterial and aspatial while still having one-or-more physical locations. Yay miracles.
Since you're writing as if you think you're waging an actual attack on the FSM, it sounds like you actually are guilty of the thing you accused many atheists of in Part 1. "Mariano exhibits a lack of knowledge of the very theism against which he argues—Pastafarianism." You don't seem to realize, among other things, that the Miraculous Nature of the FSM allows it to be invisible, eternal, uncaused, and immaterial while still having a temporally and spatially limited and interacting body. You argue that it's not uncaused based on perfectly reasonable conclusions about its physical body, but you seem ignorant of the Miracle that the FSM is the uncaused causer.
I can't really blame you much for your ignorance... most people are the kind that, if an atheist, would fall into the 'many atheists' group. Moreover, Miracles of eternal-yet-temporal and embodied-yet-immaterial are, as far as I'm concerned, junk... so I can't fault you for focusing only on one half of the contradiction, the same way I don't fault many atheists for their approach to theistic (and in particular Christian) miracles. It's still ignorance, though, and after your accusation in Part 1 it's also rather hypocritical.