I only know bio from an intro-level course, but I'm pretty sure the body naturally makes protein "markers" that differentiate your body from foreign organisms.

Try looking up some info on organ rejections. It has a lot to do with these kinds of things.

As far as your theories... I don't think we're even close to being able to manipulate tolerances to different medicines the way you describe. Just think about the fact that these medicines are mostly molecules composed just tens of atoms with very specific shapes. Those shapes and the tiny differences in charge distribution around the molecule are what make the medicine "effective" because it can bind to the proper receptors, or interrupt some process, etc.

And this is just me talking shit, the people who research pharmaceuticals every day have no idea how some medicines even work.

Your scenario may be possible very far in the future, but man I think it's not worth being concerned with it right now.