The feeler gauge is a good idea - but may be tough to actually measure, since the use of the gauge will tend to push the piston back. As far as bleeding - been done quite a few times, both by me and by the dealer. The results don't seem to change. And one point that might have been missed.. if there was air being drawn into the system I'd expect the symptoms to get worse with time. These symptoms don't. The amount of pull on the lever really doesn't change, first stroke is longer than the second, but the first stroke travel is consistent, over a period of months (and thousands of miles) of use. I did the last flush/bleed using the feature on the GS911 that activates the ABS to bleed it. It didn't really seem to make any difference.
When I had my master cylinder replaced - the mechanic doing it was the shops "master" tech, who also happens to ride an R1200R. His comment was "they all do that.." and "It will feel better for a while, then it will come back.." I know the "all do that" comment is always suspect, but since he rides the same bike, and has the ability and parts to fix it if it was fixable, in this case - I think he wasn't talking nonsense. He was happy to do the job since BMW was paying for it.
Maybe I'll try figuring out how to mount a dial-indicator so I can read the pad travel.. not sure if that's possible, but I'll take a look.