I believe I've now selected a small size microcontroller to replace the teensy on the numpad, while still keeping both numpad and TKL keyboard the same length.
Namely, this microcontroller:
The AT90USB162. Specifically with part number AT90USB162-16AUR and description IC AVR MCU 16K FLASH 32TQFP.
32TQFP is SMD, but it should be okay to solder by hand without too much trouble (I hope...).
I think it'll be possible to port the phantom firmware for the teensy without too much trouble. It's just a smaller cousin of the controller used on the Teensy2.0++ (very similar part number, Teensy2.0++ uses the AT90USB1286. Numpad only needs about 10 IO pins max, so the 21 IO pins max provided by this thing should be fine. With any luck it'll be mostly a case of changing pin definitions or something (and defining the numpad layout).
Time to acquire free samples from Atmel (the perks of being a student!), and give it a whirl on a breadboard (guess I'm gonna need to get an adapter for it too).
Seriously though. Free samples of electronics parts are awesome. If this gets produced en-mass and any of you are students, abuse it. Actually just abuse it anyway. Free electronics bits are awesome (particularly when they get sent express delivery...).