I would think it would be a practical impossibility to literally use the machine home as a reference because of the difficulty of fine tuning the master fixture (ie., dragging it around and squaring it up and clamping it down all the time). Plus, if you need two sets of fixtures for the same project, then you'd have to make perfect duplicates.....which may or may not be difficult to accomplish.
When dealing with the basic machine coordinate system, if you don't like where it is, you can move it with a G92 offset. That is the basic hand-me-down principle of having G92 still available on a modern cnc. Then you can keep all your fixture offsets as one unchanging set of values. That is the theory anyways. While you can do your level best to make perfectly repeatable fixtures based on the machine zero, I would still expect a small tweak would be required for whatever reason, and G92 would do it.
Of course, one wants to avoid the situation where the G92 command gets executed when the machine is out of position. However, that would normally only occur at the beginning of the main program. It is simple on a modern machine to execute a return to machine home on the line immediately before the G92 line, so then your G92 should never get accidentally executed at some random position.
First you get good, then you get fast. Then grouchiness sets in.
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)