The incoming major choices that are left in the first game (Stranded in Space) are situational (or case by case), meaning you can freely choose which path to take when the time comes. The flashbacks and the way the MC acted throughout his amnesia year aren't just for backstory, though. It all has a purpose.
I'd describe it like, "Hey, this is who the MC was during his amnesia year. Do you enjoy this version of him?" If so, then make the decisions that lead him to being a bit more like his amnesia-year self if a major choice allows for such a distinction, which some do, and some future ones will, too.
The history ending, as you mention it, has a future major choice attached to it, it's just not influenced by any other major choices you've made.