I don't know the NVEM controller at all, but Mach3 by itself does not do dual-axis squaring. You can write macros and things to fake it, but the best you can do out of the box is "home with master".

I have used a CSMIO/IP-M controller with Mach3 which also implemented "home with master" but did not do squaring automatically; I am currently using a PV Automation ET6 controller which has its own control software (replaces Mach3, in crude terms) which does have this capability. In other words, it depends on the controller and any controller-specific software. Have you checked the NVEM manual to see what that says? I have had a very quick look at a copy online and it does not appear to say anything at all about slave axis configuration, so I guess that you are limited to what Mach3 has.