The main difference is that Planck, Preonic, Atomic, and the rest of the boards from OLKB are based on the Teensy, which is a small USB development board built around the Atmega32u4 processor. The Model01 is built around the same Atmega32u4 processor, but in a slightly different way. To put it another way, they have the same brains, but slightly different bodies.
The Teensy is USB Mini-B, the Model01 is USB-C, and there are other subtle differences in how the body was built around it. The pin layout is slightly different, and that kind of stuff. The Teensy also ships with a proprietary boot loader, while the Model01 uses an open source one.
This is about how far I got last time I tried to look up the differences. Gave up because when I got to pin layouts, I decided that electronics is not my thing and walked away.