Very good points, all, Josh.
I would suggest that in reading the minimal info that the appeal provided, that the protestee thought that his Mazda RX-7 aero kit was a legal option from the factory. This is terribly ironic, given that I mentioned this particular aero kit this very past weekend in that other thread (and I knew NOTHING of this protest/appeal, honest), and I'm almost 100% certain that this kit was THE reason for the verbiage in the ITCS you list above.
Always remember the base premise for I.T. is IIDSYCTYC. The inclusion of the verbiage is, at best, another example of words that should not be in there (we don't NEED to state what *isn't* allowed); at worst it's a poorly-placed declaration that could lead people in the Kirk ITCS Logic Fallacy: reading about something that is "not allowed" and therefore - sometimes reasonably - concluding that since XX is also not listed as "not allowed" then it must be allowed (e.g., splitters are legal because air dams are free and there's no further restriction within the physical spaces given).
But, to your point, in the case of this aero kit there's nothing in the rules that allow it, thus no reason for that verbiage to limit it.
I think the process worked this time, and it's awful tough to get me to agree to a rule change where the worst case to a poorly-worded rule wasn't realized (same as AB's discussion on the "snake" CAI and the word "primary".)
However, if one is to consider a "removal clarification" of a long-standing rule, one has to consider if it redundant or violates IIDSYCTYC. IOW, is it telling you cannot do something that is otherwise not allowed? I'd suggest that ANY rule stating you "can't" do something is redundant to IIDSYCTYC except in the context of a rule that says you "can" (e.g., we decide to ban spoilers within the context of airdam allowances). And, of course, it's important to vet that carefully, lest you end up allowing something that is currently not allowed.
Again, I believe the process worked this time, but I see your point. I'd want to think about it further, but I'd agree with you that this rule clarifies nothing, that its value was likely historical in context, and that its removal may serve no ulterior motives...but I'm not so arrogant as to believe that I've thought through all the possiblities...
GA