What's in the .RTC files and why is compatibility such a big thing? Honestly it's in everyone's interest to discourage emulator-hopping lest it cause weird bugs that don't otherwise happen.
It appears to just be 20 bytes of internal data, see bsnes/src/chip/srtc/srtc.cpp line 98. I don't believe, from looking at it, that it could cause any emulator-hopping bugs, since it's all just a bunch of UINT8s.