nolansneeder,
I think I was where you are about 2 - 3 years ago.
I designed a board with all of the interface circuitry (12V to 5V stuff, signal conditioning, 232 TTL to transmission level, LED drivers, etc...) on a SMD board, but put the Teensy on as a through hole component (along with DB9/15/25 connectors, etc...) that's added after I put the SMD components down.
I use Upverter with great success (upverter.com). Design board, send of to OshPark for a PCB and Digikey for components (or PCBWay in China for a complete PCBA - stuffed).
I got a small $11 hot plate that can do a 2" x 4" PCBA reflow quite well. I also get the stencils from OshStencils...
I've made boards that I would be happy buying from a professional source, at home. My projects have been system monitors for an RV, and my latest is a 30 channel data acquisition / display system driving a 3.5" touchscreen display that I use in an experimental 200+mph airplane. I've been flying with this for 100+ hours of flight time so far with great results. (simple, 2 layer PCB use in the above system. There's a second board and Teensy 3.6 that goes next to the engine that talks to the board above via RS232 that collects temperatures, pressures, etc... in the engine compartment.
These Teensy's are AWESOME, and I'm a hack at best so to be able to build things like this at home, Paul has given us a huge foundation to build some awesome projects. I may, in the future, try to do as you are suggesting and build the Teensy functionality right into my board, but I've got some learning to do before I try that. Taking the smaller step of installing the Teensy onto a PCBA was a great step for me before going further, and it gives me some awesome functionality easy.
I might even consult with an electrical engineer who knows something about laying out PCB's.