Every thing you said Kit was spot on except for this bit, but your excused with you being a Linux Geek..:beguiled: But I'll clear it up for the sake of those new to Mach3.
Hitting REF ALL works in 2 ways depending on Home Input settings. If the HOME inputs are NOT enabled then REF ALL will ZERO the HOME position where ever the machine is parked.
But if the HOME Inputs are enabled then REF ALL will start the HOMING Sequence(macro) and the machine will set off looking for switches.
So you MUST use REF ALL to set MACHINE ZERO which is the bit KIT doesn't know with not using Mach3, just be careful if you have enabled the HOME inputs as the HOMING sequence will set off and Mach3 as no clue if switches are fitted or not so will keep moving until it hits a something.!!
Not fitting HOME switches is crazy unless you have repeatable hard stops because they are life savers on jobs when a cutter breaks or power goes off in middle of a job etc. They allow you to get back to zero or any point in a job easily and accurately. They also allow you to break large jobs into separate sessions at the machine ie: over a few days and repeatably get back to WORK ZERO or a line you stopped the job at.!