I think he is describing two things that were done ...
I think he is saying that every box / fixture receives two pieces of MC. The fixture is then hooked up to, say, the red wire from each cable. Back at the panel, one red is landed on, say, phase "A" while the other red is landed on phase "B".
From a code perspective, there is no requirement to adhere to any color coding. So, having the reds land on two different phases is not a violation. A maintenance / troubleshooting nightmare, sure ... but no violation.
I don't think there are any neutral currents involved at all.
There is a violation of the code requirement that all conductors be run in the same conduit or raceway. I believe the reason is a fear of inductive heating of the raceway itself.
Our OP is thus presented with an old installation that has been working fine for years, and is wondering just how important it is to fix it. This, naturally, would be an involved and disruptive task.
I say: Do it. I suspect that, along the way, other, more critical errors were made. The method smacks of 'self taught, well meaning handyman.' I am curious as to the use made of the white and green wires in those cables.
