I see in OS 5.3.1 there was a PR to remove the pullups on the serial ports [rtl872x] Dont enable usart RX/TX pullups by scott-brust · Pull Request #2646 · particle-iot/device-os · GitHub
I can report that I am now able to communicate with my TMC2209 modules.
For anybody else who wants to use these modules, this is the hardware setup that I have working:
Two FYSETC TMC2209 V4.0 modules, in “daisy chain” configuration where both modules TX/RX are connected to Serial 3 port of the P2. This allows one serial port to control two modules, provided that the address pins (MS1, MS2) are configured to be unique. This is how I have them configured:
I am using this library with success. GitHub - teemuatlut/TMCStepper
Thanks for the help!