AccelStepper, FastAccelStepper and MobaTools all mainly focus on control of the motor on the STEP/DIR pins, leaving the control of the microstepping configuration and current limiting to other (often physical) interfaces. The TMC2209 allows configuration of the microstepping and current limiting with the UART, but does not require the STEP/DIR interface be ignored.
See pages 4-5 of the datasheet about the three modes of operation, and how the STEP/DIR interface is available in all of them:
This way, only three signals are required for full control: STEP,
DIR and PDN_UART.