Standard disclaimer - You do you with your tools in your shop. I’m just providing my opinion.
As I understand it, the benefit of the MFT table is that you can easily set up jigs or fixtures on standard spacing and angles to allow for work table flexibility. Since the MPCNC feet only need to be attached once, I don’t know that there’s a lot of benefit to developng a complex jig. I don’t think you’d be able to just slip the upright legs into holes in the base without securing them in some sort of foot.
What problem are you trying to solve?
If it’s to be able to have adjustable height, then you can bore the pass-through holes for the extended legs oversize, and precise placement of this hole is less critical since the feet (which are secured to the base independently) control the squareness of the rails.
If it’s to be able to quickly change the spacing of the rails (e.g. have a smaller footprint to improve rigidity when working tough materials), I’d probably just print three extra feet that I could attach where desired to establish the smaller machine size. For simplicity’s sake, I’d use the X Min/Y Min foot “as is” and I’d have one additional foot along each of the existing X min and Y min rails so they were outside of the working area (these could stay permanently attached depending on your leg height), and have brass threaded inserts for the last “temporary” foot’s location which would end up inside the working envelope of the machine when it was in its larger configuration.
If you’re looking to establish a standardized grid for aligning work, I’d get the machine built out and then use it to bore the holes. No jig needed, and the programming of the job would ensure parallelism to the machines axes.
It just occurred to me that you might be thinking of boring out 4 (or more) of the MFT holes to use an existing table as the basis for a temporary MPCNC. Intriguing idea, but I’d be worried that the rails would get twisted or bent when setting up/tearing down or while it was in storage. Right now, my Burly (cutting area about 12"x20") is mounted to a 1/2" plywood base with a 3/4" MDF spoil board added on top, and this is simply clamped to a counter top in my workshop. If I need to reclaim that space, I can pick the whole thing up and hang it on the wall without worrying about it getting out of alignment when I put it back in service.