All you need for a fixture plate is a method for locating and holding the part and a feature to zero off.

I use dowel pins for locating, all you need is enough space on what will be your bottom surface after the flip for drilling two dowel holes. For fixing I don't think I've ever made anything that doesn't have a spare hole or two to put a bolt through to hold it down, on your cases you could just use stick a bolt through the big square holes with a large washer to grip the sides (one of the clamps that came with the OMIO would do). When you need to do an op on/around one of those bolt holes you just program a pause in your toolpath, move the bolt elsewhere on the part and carry on. For x/y zero I drill and ream a nice round hole to zero off, this is obviously at a known location because you have modeled it in CAD, the same goes for the dowel pins, and therefore from your X and Y zero feature you know where everything is to within the tolerance of your hole and dowel pin sizes, which I've never been off more than 0.2mm across the full 355mm length of the X. Z zero for me is always the top of the fixture plate, then when you're facing down the top of your part you know you are bringing it down to an accurate size.

If that makes sense?