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I have zero issues with 'smaller' extruder motor and I use fairly low vrefs (0.76 on extruder) compared to recommended https://youtu.be/7VHwcEroHPk?t=253 (I also have TMC2208)
so you could always increase if you get skipped steps
I've replaced it with z-axis instead, drilled 2 new holes since default rod wasn't aligned anyway (common problem on original ender 3)