Maybe I'm missing something, but in 1.2 I could simply construct new citizens ad nauseam . My home planet had 650 citizens at some point, as my morale would allow for it. I didn't transport them there, I just built them. Never noticed population going down, perhaps it did. My cap was 150 or something. Does 1.3 at least stop you from building past the cap?
As Ryat said, yes you can build above the cap, but you have to drop your pop below the cap first. If you're the tiniest bit below the cap, you can build an assembly project to take you above it. You can then offload the extra pop onto a transport or colony ship and build another assembly project.
When you reach your desired pop, you can land the transports, reap the production benefits and send those transports to another planet to continue their nefarious deeds.
Your excess pop will start to die slowly, but the added production can make it worth your while.