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.
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 :(