Regarding the shortage, I find it really annoying, that no matter what steps you take, you cannot prevent it. Totally agree that Gamma cores are a barely, if at all useful for colonies. They have their use as "friendship tokens" or memey, Glimmer wolfpack fleets, but that's it.
Betas are in a weird place. For colonies, if you want an industry where you can meaningfully put them, you want to do that temporarily at best and then switch them to an Alpha asap. For ships I think there is a good use of a few, but chances are you are going to turn most into reputation or credits.
Alpha cores on the other hand are generally speaking excellent for just about every industry and even for spaceports, stations and such. You won't be able to use many of them for ships and they have a way higher value used for colony stuff than having turned into credits or rep. Unless, of course, when you are at the point of farming them by the dozens. But by then you've practically won.
TL;DR
Gamma and Beta cores are indeed quite underwhelming as colony items. Could possibly use a bit of buffing in that regard.