I think i may have gotten a little carried away trying out this mod... I'm not even sure when i started.
Does buying up all the AI personnel and supplies actually adversely affect their spawns? I couldn't tell for sure. Once i put it in my bases it'd spawn one or two large fleets the next day.
Is there a benefit to choosing pirates? Or is it self imposed challenge mode?
If i choose hegemony and a brown hegemony fleet shows up is it my ally? I haven't had a chance to interact with that fleet yet.
Fantastic mod
I'm excited about .3
By buying resources from the AI station you'll stop them from building fleets, but stations replenish resources and convoys deliver them so that may have happened in the meantime.
Pirates (and a few of the other factions) are definitely more difficult to get very far with! I'm undecided whether to tweak that too much at the moment, as it does rather nicely give different difficulty levels...

Hmmm the last scenario you mention shouldn't be possible, and it hasn't in any of my testing... Can you please make sure both you and them are Hegemony? If you both are then that's a bug...

However, Rebel fleets will impersonate a faction and will be named something like "Rebel Hegemony Blockade Fleet", and they will be at war with you (if you are Hegemony) so that maybe what you are seeing?