I just tested it and no conflict so far ^^;;

actually would it be compatible with Themed Colony Deeds since it renames not just the base colony deed to be the Apex ship colony deed but also the Avali version as well (though I think it just add's it's own version of it)

I was gonna say the same with Tenants Reworked ^^;;

If the mods in question are working off of scripts that the colony deeds pull from, they should work the same.
If the mods are modifying the deeds themselves, then these won't have those changes as that'd be on a per object basis and these work off how vanilla colony deed objects work.

Is this compatible with the rest of colony deeds mods? Like The Tenantator, Colony Tweaks, etc

alright happy to see someone still making mods