I did some more careful testing with the multimeter and found that the 3 jumper pads above the ISP connection do actually connect individually to MS1, MS2, MS3. I must have made a mistake when doing the continuity tests the first time since the pads are so tiny. This means any microstep configuration is possible. I confirmed this by shorting the middle jumper (MS2), which gave me 1/4 steps. I just want to update in case anyone else needs this as the info in this and other threads about only having a jumper for MS1 seems to be wrong. This module is great. Since you are able to program the atmega328 on board, it's like having a mini arduino uno with stepper drivers built in. Totally usable standalone without the M5Stack core.
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RE: Stepper Module