That's neat.
I've been experimenting with some rubber inserts in the keycaps made from some ~1mm rubber sheet I have easy access to. The results were somewhat promising (softer, quieter landing, not much travel lost), but not even enough across keys. The sheet needs to be half a mm thicker to work right in the keycaps, but even then, it's a pretty messy solution.
Your solution will surely produce better, more uniform results, with the added benefit of acting as a muffler inside the keyboard, reducing all sounds much like the pads underneath the keyboards some people use here.
I have a Filco now, and may buy an ISO G80-3000 soon, which would have the exact same layout as yours there. If I do, I will definitely pester you for a ready-for-printing image file. Maybe I'll use the 1mm rubber sheet for ultimate damping, or something a bit thinner so that I lose less of the travel.
By the way, how much biggger are the keycaps than the base of the switch? If they are, say, 3mm larger across, then there is a 1.5mm spacing on either side, which means you can afford to just make oversized cutouts for each switch (say, 0.5mm or 1mm larger than the base in all 4 directions) and still be sure all of the keycap will land on the mat. That buys you some room for error with the placement of the holes.
I'm not a fan of the rattling of the Filco, so the thicker caps on the Cherry, pcb mounting instead of plate mounting, plus a sheet inside the board and a mat underneat should work really nicely to muffle the clack-clack. I have browns in my Filco now and want blues, so these mods should at least make sure the new keyboard is not that much louder than the old one. Or so I keep telling myself.