That's interesting. It does appear that the Smoothstepper plugin for Mach 4 has no place to set pulse widths. And your issue does appear to be related to the control signals. There is a slim chance that it's RF related if the control signal is traveling a longer path from the Smoothstepper than it is from the Arduino, but honestly I'm 99% that 109jb is correct and it's a pulse width / timing issue. That is a far better match to your finding about the error always being the same; RF is typically far more random.

You might also look at:
https://www.poscope.com/product/pokeys57cnc/
if you don't mind shipping from the EU.

Both Planet-CNC and pokeys are PMinMO compatible BTW.
techref.massmind.org/Techref/io/PMinMO.htm