After all, the 'heat shield' is a automanip which constantly sets your temperature to a particular number. Not to mention that they have a very exact area that they modify.
And that's only the countermeasure for temperature. I really don't know how you'd safely prevent someone from using a vector manip to mash your brain- constantly using a vector automanip to set your brain's velocity to zero... seems like a really bad idea. It might work for something like an avatar pilot, where there's no real movement, but how would you use it in a battlesuit, let alone an MK?
They don't set something to a specific variable. They simply prevent extreme/dangerous modification as much as they can. So if their sensors sense something trying to heat the area you occupy in a dangerous way, they activate the automanipulator to negate that change.
Of course, there's the question of
how they sense the modification... Probably using some sort of space-magic-sensing like the trick Amp Specialists use to see with their amps but in manipulator form. Or maybe the change is gradual enough that normal sensors have enough time to sense it and trigger a counter-response from the automanipulator.
Manipulators can't be operated continuously, not for very long. Even doing so with amps is very strenuous for the one that does it. Same with automanipulators.
Plus, I think not allowing your body's temperature to change would have some very bad implications. Most chemical reactions that happen in the body give off or absorb heat, so stopping all temperature changes in your body would probably screw its chemistry in some way.
Remember, it's not that automanipulators can't be programmed with variable outputs and inputs. See the kinetic amps. They accept variable input and give off variable output.
We just don't have access to those kinds of variable automanipulators. And if we try to modify a manipulator/automanipulator/amp, it will most likely self-destruct unless you make a very good roll (or not even then depending on what piecewise wants).
EDIT: Hmmm... What if piecewise has some hidden counter in his notes and every time someone uses an amp or manipulator he increments that counter and then throws something at us when that counter reaches a certain number? Or maybe a future succeed-or-TPK/succeed-or-you-loose-the-game mission becomes much more difficult every time that number gets incremented. Kinda like Zentol in Perplexicon.