Again not getting into Mach v Linux I use both mill Linux and router Mach.
One big difference is that Linux will pause almost instantly while Mach has to empty it buffer (that can mean the machine can run half the table length before it will stop). I think you can get motion controller card for Linux.
You are right saying Linux won't do the homing with twin axis. That was one reason I had to go with Mach3.
Mach has the more user friendly front end. But both are good. ..Clive