One thing I want to suggest is to at least make the exp outside of nebulas feel like something. The problem I had with the model is just the fact that I get what, only 15 exp for each guard post and for the command station I think? First, on low difficulties, you really encounter only just a couple guard posts. And... assuming you did a nebula before killing anything outside of them, the exp that you earn is extremely underwhelming. I am not asking for anything like ships giving exp or something to that effect. What I do want, is to feel like the champion can gain a little something for being helpful outside of its own ventures. Otherwise, its solo ventures are the main appeal for a long time.
I wouldn't really know how to fix this. I know someone hinted at a suggestion of re-adding AI turrets to the game. If the AI got turrets, that could add to the exp earning game quite enough (first kill of every turret rebuilds not counted or something). On the other hand, I don't really know why they were removed in the first place! Maybe this is a terrible idea to even consider. Guard posts could just be worth MOAR EXPs, but that wouldn't really help either because then you have to bring the champion on every raid into AI territory or lose out on so much exp that you may as well be getting punished directly with that huge exp loss.
Ultimately though... I feel like exp out-of-nebula is not just underwhelming, it's not viable. I don't expect to be getting every module but I do want some growth for doing everything. While I say that, I'll totally admit that I might be completely off base here. It might be worth starting a poll when the whole working out the point earning and spending parts of your plan like you mentioned, just to see how everyone feels.