I just think the idea that EVERYONE who didn't want to be affiliated just up and left(or died )is hard to buy.
I get why- toy franchise, based on one team vs the other, character designs are largely based on toys or expected to be made into toys, so making unaffiliated citizens goes against the point, and requires more budget than Hasbro is willing to spend for what they don't see a point to.
. Even this is nuanced, because war and conquest isn't evil to a conqueror, only the conquered.
Exactly, so why he revels in his actions he still sees his way as justified. The very first piece of Megatron characterization we have, before the show or even comic was out, is his motto being "Peace through Tyranny." It both shows him having a sweeping, organized goal and also harsh ways of reaching that goal.