The game just told me I cannot use freighters to boost alien populations with anyone but themselves.

The usual MOO2 trick is to settle a subterranean species on your own alrady full planets. ISG only has this lousy vault.
How could they forget about population mixing in a "spiritual successor"?

The feature even has potential for improvement, like getting a percentage of all the other races traits with each assimilated population unit or diplomatic ways / galactic events to acquire alien pop units for example ...

+1 to that.

I'll add that I'd like some improvements like more info being more readily accessible in the map.

Hello, thanks for the reply here on gog and for the game, too!

well, I assumed from the tooltips which show assimilation status per pop unit that the units would be handled separately. But the distinction probably doesn't go into the core mechanics like production/research/morale calculations.
Maybe the calculations for mixed colonies can be wrapped somehow, like e.g. calculate each planet separately for only one species (like it is now) and then add up the results of all species for this planet? Or use a "mixed factor" like a mod?

Concerning the biome preferences you can use a curve for balancing, so the first couple of units would be affected only a little bit by biome penalties (every planet has some regions of other biomes like polar caps and deserts, enough for a few pop units). But after say 50% of the planet space or so the penalties would kick in more and more.
Your tidal locked planets inspired me on this idea, which is the extreme example: A species which likes it hot would settle in the otherwise empty day area and another species on the night side. This means, of course, a higher max population cap than before.
All of this applies to every planet more or less, because they all have some unused climate zones.

And the challenge for the player would be to find the right mixture and set up the strategy accordingly.

The main issue right now is: Having a conquered race in the empire feels like a game in a game.
I haven't tried it yet, but I strongly assume they must build their own colony ships although there is a bonus for building colony ships on the empires (not the species) homeworld. It would help to select the race for colony ships so it doesn't matter where they are build (requires a freighter during build maybe?).
The population boosting mechanic with freighters doesn't fully apply, it is restricted to other planets of the same species, which adds to the isolated feel.

Mixing alien pop units with already assimilated ones should have a positive impact on the local (!) assimilation rate.
And I wish for a culture decision like Enslave vs. Assimilate, so I can construct my evil dictatorship in style :-)