(;-) Machine Zero can be anywhere and in many cases it is NOT at teh end of an axis it can be in the middle. It is not tied directly to home(G28) as HOME can be anywhere as well. HOME(G28) is just referenced off of Machine zero.
The only direct link to machine Zero is the G30 that will take you to Machine Zero in MACH3 gcode.
The Machine coordbase is there so Mach knows where it is at in relation to ANY offset that you may require. Once set the OP cannot change any value the most they can do is Zero it another location(not always a good idea)
BUT don't let that confuse you(;-) Yea Right. Just set up the machine as you want it to be and sling some chips. Once set up it will always behave as you set it up. If you find out you don't lke it that way, simple change it(;-) that is what config and setup is all about.
If you want it to conform to the perceived standard do so(;-) or not(;-) your choice.
BUT if you set it up weird so you are the only one that can understand it THEN only you may be able to understand it. Catch 22 The rest of us may just say HUH?

??
(;-) TP