It doesn't really make any sense how this could possibly be related, and for that reason I don't rule out some other factor being at play, but the correlation has been pretty evident on all 3 occasions when I tried to do this and the absence of the same effects when I don't do this and instead do pre-boil the pasta all seem to point it being the relevant variable.
Assuming the no-pre-boiling somehow is responsible, the obvious solution to the problem is to just stop doing that and indeed I have for fear of a repeat of the horrible experience, but it's just that the ease and efficiency of the method is so appealing and I would like to try it again, but I also really don't want to gamble on that unless I can be pretty well assured that the results were unrelated to the lack of a pre-boil or if that actually is a plausible cause, I'd like to learn by what mechanism this could possibly play a role and why it doesn't bother most people.
Boiling the pasta removes some of the starches from the pasta, which is why people recommend adding some pasta water into your sauce. Maybe you're allergic to those starches?
Or, maybe it was an overload you weren't used to. Definetly think the starch is the issue.
I did wonder if starch might have something to do with it, because not long before those incidents I had another similar experience when trying to cook fried plantain to go with a steak. I didn't really cook it enough and it was a little too firm, I wasn't the only person who ate it, but I was the only one that got very sick and I had read something about "resistant starch" in plantains making some people sick like that.
I cook and eat pasta a lot though and I often deliberately add starchy pasta water in the sauce too, but I guess maybe that's not quite as much as one gets from the no-boil pasta bake method. Good theory, cheers. I guess in light of that idea, that is a plausible mechanism and that probably means I'll have to continue pre-boiling :(