Its ok, I was mostly just concerned with the sound piece. From what I can tell the rom dump is almost identical between the version in ram and the version from the converted rpx, which suggests that the VC is not patching the rom first, but is instead applying the patch some other way.
I'm on the same hunt as you, ootnes2. In the past, I've used vcromclaim to extract purchased SNES VC titles and found that it handled the sound by extracting the PCM audio, converting it to BRR, then injecting it into the appropriate places within the resulting .smc file (more info here: https://github.com/Plombo/vcromclaim/blob/master/snesrestore.py). Unfortunately for me, I can't even find the file in my decrypted 3DS VC title (Earthbound) that contains the PCM audio. I figured it would just be within data.bin but I am not seeing any PCM references in there. If you find anything more on this, please let know.