Got an answer on the Mach3 group.

A: Depends on your drivers.
"Reverse" under Homing/Limits is correct for all drivers. (this however was a recent change)

On some gecko drivers you use active low, on the others you do not.
Gecko 203V- Active high
G 201- Active low
Haven´t tried 25x, 54x, but geckodrive says use active low. YES - It
makes a difference.

With some other boards, it may or may not matter.
It may make your system work poorly/flaky if you do not use the correct
setting !