So there are two mains circuits, from the main junction panel, one to each box? Are these metallic conduit? (If the line filters are doing their job, this shouldn't matter.)
You didn't list more connections, how do "Metal box 1" and "Metal box 2" connect to "CNC machine" and "CNC stand"?
Is "CNC machine" just sitting on top of "CNC stand", as the names suggest? Is the stand incidental, or is there anything electrical on it, too?
You also later mention a ControlBox but didn't say how it connects.
It sounds like you're being very paranoid about ground loops, as in safety ground. I don't know of any problem with bonding already-grounded appliances together (but, someone better versed in CE code, do chime in?). It doesn't sound like you're measuring tiny, low-frequency signals between boxes, so ground loop (as might apply to audio systems) is a non-issue.
The reason I'm asking very precisely is, whenever I see "star ground" I am
instantly suspicious. Star grounding is
almost exclusively applied badly. Like slotted ground planes, it's a massive pitfall for newbies. Yes, it's a thing; and the designer should know about it. The technician even, say when it comes to pro audio systems, or setting up lab or test equipment. It is a possible option, another tool in the toolbox. But as with all tools, one must be keenly aware of its conditions, traps and downsides. And these gotchas are far more numerous, for star grounds and slotted grounds and such, than the benefits are. And because there are so many gotchas, it's very likely one or more will always be missed.
It's an electronic design equivalent of
Roko's Basilisk. It's literally a kind of story that is better left untold, so people don't try to use it just because they, I don't know, think it's neat?
So that's where I'm coming from, and just want to sanity-check here.

By far, the biggest sin people commit, regarding star grounding, is the same problem as with slotted grounds: running connections between sides, rather than following the ground path. Crossing traces over a slot, takes exactly the current you meant to avoid, and puts it into the traces (or vice versa); connecting a cable between two boxes, that are star grounded separately, creates a loop that's altogether worse than, say, routing the ground with the cable itself (or, better yet, running the cable and ground together through a conduit).
So, at this point, it seems like you'd most benefit from using metallic conduit (flexible if needed) between the various boxes and machines, so you can get the drivers' noise currents back from the motors, inside a conduit, rather than with a huge loop around all kinds of metalwork, that will radiate. Or if conduit is unacceptable, filtering the offending sources (but, that's probably even less practical -- you can't simply hang a line filter on a VFD output, unfortunately).
Tim