not quite sure i follow the last part of the question.
essentially what a time machine/time capsule back up does is creates it own virtual disk on the drive and nothing in that "virtual disk" can affect anything outside of it, in essence things as applications or unique serial numbers for each machine. its all specific to each machine so it wont have anyway of affecting the other back up or mac.
now if you want to restore your affected mac with the OTHER Mac's time machine back-up, you can absolutely do that - when you reinstall the OS choose to restore from Time Machine back-up and it will appropriately place your content over form the back-up source you choose.