EAGLE is, at times, the best puzzle game ever. "Oh, wait, I think I can do it shorter/better"
Yep, that feels good. Remember, don't be put off by silk on the top panel: you can get a decent amount behind those jacks. The only things you mustn't overlap are the through-holes. But I reckon you could do a lot with the CVs, too. One-thing-at-a-time is a good way to go, though.
I'm presuming given the 06xx and 08xx you're assuming this will be assembled, rather than made by hand? (1206 is fine for doing by hand, you see).
I might have a crack at that, just to see if it's possible - the opamp and so on on the top board.
The problem with 'under and behind the Teensy' is that if you leave the USB connector facing downards, you're left with having route things between the gaps in the pins at the other end, which isn't a lot of space - there's not room to come out the sides. Although: you have got two sides, and surface mount components, to work with.
Happy to keep diving in: like I said, it's a fun puzzle to play sometimes!