We do sell a Mini54 chip separately for people who want to make their own boards. It's normally used as a stepping stone to volume production, where you're making enough of whatever you've designed with Teensy3 that buying the PCB from PJRC isn't feasible, but not yet enough to invest the time/effort to some other programming solution (eg, buying something from P&E Micro or writing your own programmer using EZ port or some other way).
The Teensy3 code in Teensyduino, the part that actually runs on the MK20, doesn't depend on the Mini54. And even if it did, that code is all open source, so you can modify it to suit your needs.
In theory, it's probably possible to separate Teensy3 into 2 circuit boards. But the USB connects to the MK20, not the Mini54, so the board-to-board connector would need many pins for the all the signals between the chips and also the USB. The wires and connectors would need to be capable of 12 Mbit/sec USB. That's probably more cost and complexity that the meager savings from not having those other boards on every board.
I also personally like having the board "just work", well, with the right USB cable and a computer. At least for now, I'm not very keen on the idea of a 2-board solution.
I do have some ideas about low cost solutions. I can't talk about details now, but when/if that ever happens, it'll be designed to preserve the usability and ease-of-use people expect with the Arduino software.