keeps commanders relevant as more then just a resource generator especialy lategame
Trying to make commanders relevant in the lategame, whether it is by giving them free upgrades or any other mechanism, poses a fundamental problem: because your commander is irreplaceable, it encourages players to be timid when expanding with their commander in the early game, and results in even harsher punishment when you lose your commander to some cheese like Widows, Ravens, etc.
Expanding with your commander will still
probably be the correct gamble to make, but the punishment for losing that gamble being "you lose access to free cool upgrades forever" is a feels-bad moment. Losing the free income already feels pretty bad.