Carmack has always made his engines for ID first. sure, they've licensed them, but they weren't designed with being licensed in mind. they only ever included what ID needed for their next game.
Epic on the other hand designed their engines to be capable of just about anything, to allow easy movement of content between versions, to be modular so as to allow a developer to write their own renderer, but still use the unreal tools... and much more.
the Quake 3 engine that Carmack built didn't allow for mid level saving. because Quake 3 Arena didn't need mid level saving. so they didn't code it. licensees had to code it. ID Tech 4 was good at making games that looked like Doom 3, because that was all it was coded to do.