That's true that it takes up 1 slot, but it is also true that it would also give you something in return.
And it could be unique for every faction, not to mention that you can actually relocate it if it is that much in the way.
Also, I don't think that 1 or two lost building slots would be a mayor problem.
These buildings could only be built in planets specific for each faction, giving each faction(including the soon to be 6 imperial-based factions) some uniqueness in GCs.
And that 1 lost building slot is really not much.
Most planets simply don't have enough openings for ground buildings to make it ideal (so they're not useful for production), so adding ANOTHER building in that you needed to build on your capitals...
Well, if a planet does not have much build slots, why would you want to make it a manufacturing planet in the first place? IMO it is a waste of credits. In fact, most of my planets are standing empty on the ground. I played the game so much, that I came to the conclusion that it is ineffective to build up every planet. Invade, don't stuop and go to the next and you don't have to build it up. Just when you decide that you need to build m up a place because your main manufacturing planets are so far. You can move troops in the galaxy for free after all, but time is still precious.
I myself have divided the galaxy onto 6 areas in the Imperial Civil War GC and in the Art of War, and have 4 planets that are dedicated to production. That's 24 planets out of 100 at worst, and if 1 of those sectors become so distant from a front that it does not worth it to even try to build it up then why should I? Just kick the enemy out of there and done. for example the EotH territories as remnant after stomping the PA as remnants.
And as a trooper production planet is enough to have 3 slots since infantry gets done pretty fast.
So all in all, i don't think that losing 1 building slot would be that great of a deal.