The values entered in those fields is the amount of time to be added to the standard pulse width (around 3uSec). So if you enter 5 there you will get an 8uSec pulse width. I think it is only true for the step pulse, the direction signal being just a change of state, but am not sure about this as some time ago someone was reporting a different behaviour (although with SmoothStepper) which was never confirmed by other users.
If you need a wider pulse than that then use Sherline Mode (under Ports and Pins), which will give you around 20uSec pulse width.
Something I had forgotten to mention before I started this run of parts - would you consider adding a parts counter DRO? Should be fairly simple and you already have a macropump anyway so will only have to look at the Cycle button being activated and count it.
Another thing which may not be that simple is a total elapsed time DRO (from the moment Mach loads). It has to be zero-able. Together with the part counter it can be a very valuable tool for high volume runs.