This sounds great! IMO long build times have always been a little problem, and combining star bases of the same level seems to be a good way to speed them up if you have the extra cash.
I'm just a little concerned with making the space colony unarmed, but vital for the survival of all other buildings. Don't you think that this will encourage "colony rushing", i.e. just ignoring the defenses, focusing all fire on the colony and then hypering out when it's destroyed? I'm OK with the colony being a requirement for building construction yards and golans, but losing everything when the colony is destroyed seems a bit harsh.