With the Teensy you have the freedom to wire the matrix any way you want it, and to configure function layers which are a must if you make a 40% keyboard and more or less half the point of making custom keyboards imho. If you're making a 40% keyboard you could probably get away with using the cheaper Pro Micro instead of the Teensy 2.0 and still use the TMK firmware, but it's a bit more difficult to reprogram.