I have R7 shoes, but no custom footbeds. I can't imagine that the footbeds are glued in that well, but if they are, I'd leave them alone.

I can tell you for a fact that is possible to attach the speedplay cleat directly to the sole with no adapter plate because I have done it. I drilled and tapped holes for the M4 bolts, directly into the carbon sole.

One problem with doing this will be no fore/aft adjustment possible after it's done, so you have to know where you want the cleat positioned. There will still be side to side adjustment.

The adapter plate does two things - adapts the 3-hole pattern to 4-hole and creates a flat surface for the speedplay cleat instead of the typically curved surface.

When I made the alteration to my shoes, I used epoxy putty and 5-minute epoxy glue to create the flat surface - basically doing the job of the tapered shims that go under the adapter plate. Once that was done, all I had to do was bolt the adapter in place and drill 1/8" holes right through the nuts in the adapter plate and then run the M4 tap through the adapter plate, just like installing the 4-bolts, but using a tap to cut new threads.

It would also be possible to install thread inserts into the carbon sole, but as you've noted, the soles are thin and finding just the right thread insert can be tough. I bought a few candidate from McMaster car just in case I ever strip the threads in my shoes, but I might also just drill the hole a little larger, fill it with epoxy, then redrill and retap.