Ultimately, a level will be perfectly (and I should stress perfectly) balanced if and only if both teams are placed in the exact same situation. A perfectly symmetrical level is balanced because each team gets exactly the same things (the only difference is that one side is mirrored, which does not affect balance).

By this definition, a level like you just described cannot be absolutely balanced. Even if it contains a symmetrical portion, the teams will be placed in slightly different situations because (and perhaps only because) their spawns will be in different places. You could of course remedy this by spawning both teams in the same spots, but that would be highly unusual.

This is all theory, though. In practice, you can make a level that is balanced enough (not perfectly balanced, but enough for competitive play, which is the case of most levels) using the concept you just described. You would just need to design the non-symmetrical part of the level carefully, and pay attention to where the spawns are.

As for your question "would it make for an interestingly varied and balanced ctf level?", I don't think it's a matter of "would it?" but "does it?". After all, we already have two CTF levels (that you named) which fit this description, more or less. We need only to look at and play those levels to see if the concept works.

In my opinion it does work, although it could be implemented better in both of those levels. Undulation has multiple warps to the base area, which makes it harder to defend (although the bases are somewhat camp proof, which helps). This can lead to a feeling of luck when it comes to scoring a point. One spot does a bit better by only having a single entry point, but the base area is too small and cramped, and is campable (warp + small box + camping is usually a bad idea, especially when said box contains two bases).

Probably a "perfect" solution would be to use one spot's entry point into the base area, and combine that with undulation's anti-camping system (it is best to discourage people from hiding in a warp area).

Interestingly, I actually have a sketch of a level which I was planning to make this month, basically using this concept. I've been planning it for quite a while, but have been putting it off due to the strangeness of the concept.

Strangeness is actually the main problem here. This is a neat idea that can lead to neat gameplay, but it is vastly different from normal CTF (more than your average gimmick; it changes the gameplay in a way that it almost becomes a sub-type of CTF rather than standard CTF). Thus, not many people would play the level unless you got someone to host it.