We do plan to have certain planets get different effects based on certain canon information, some more passive (ie the Allegiance stuff you're talking about), some more active (like Centerpoint perhaps). Ingame, this will usually have to be based on structures with abilities though, so we want to be careful not to overdo it if it ends up causing extra lag.
I think using allegiance to reflect this is a bit limited in scope. I'd prefer something more like what EaW does with restrictions on base sizes/logistics slots.
Keep in mind that planets in Sins are not coded individually, so slot amounts and upgrade limits are not something you change on an individual planet; they're an instance of a type. This also tends to help with burden of knowledge, since you'll eventually know that Swamp = this many slots, Oceanic = this many, etc, which is more intuitive than Kamino looking exactly like Mon Cal but having completely different functions without any visual indicator for that information; having these differences communicated through structures tends to make the game more intuitive anyways.