I think you can only get to the number of rows on a 2KRO keyboard before you start getting blocked keys.
The reason the modifiers are usually available for three key combinations is normally because the matrix is optimised for their use. I have been thinking about a model M and getting it NKRO. The biggest barriers are getting either a PCB or flex PCB in that size and finding somewhere to put the diodes (there looks like there's room under the ridge of the barrels. Otherwise, you'll have to cut holes in the plate or barrel plate to fit them)
I've always wanted an M industrial, so maybe I'll bid on one of these. If not, I'm sure I'll find one somewhere (I might have a deal already; we'll see if it goes through)
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On my soarer converter, I went without pins, soldered the DIN connector to the holes and then press-fit mounted it in an enclosure. If^H^H when I were to do it again, I might get an aluminium housing and one of those neutrik USB connectors and make it "pretty".