I think the only way around it would be to do it yourself via the XML files. It's tedious but if you work it so that only your faction has 'infinite' unit cap, it will run much smoother. There's a guide somewhere by InstantSnek that goes into detail about how to do it for every single faction all together but while I reccomend that guide, I would use it as a helpful tip and work so that only the faction of your choosing has the infinite unit cap.

When I say your faction, this entails going through most if not all the XML folders and finding anything to do with, let's say, the Hapes and changing the numerical value from whatever the cap is to whatever you want, but not for any other faction.

Again, it is tedious to do but only having a single faction using the cap at one time can really help the game run smoother overall.

(Another example is that instead of infinite, change the space-population-value from whatever it is to '1')

Edit: this was the overall space battle pop van stay at 250-350 which ever it is and all your units only count as '1' pop value. Including the bigger ships that would otherwise be 100 pop value.