Wii U VC does the same, I know for a fact since I dumped EarthBound through RAM to get the already patched ROM and it does have modified lines.There something i should have mentioned before that may help but In the past the VC games on wii, (Wii shop channel) People has found out that some games use mods, in the form of plain text asm patch which are considered On-the-fly Patching, for reasons like fixing problems in the old games or adding new features to it.
Here is a example for phantasy star 2 difference in the original genesis and the nintendo Virtual console.
View attachment 53484
Also here is the link to the page with the plaintext asm code, I do not own any of this credit, just wanted to share if it may help.
https://tcrf.net/Notes:Phantasy_Star_II
If you look at the RPX file converted to ELF with a debugger like IDA Pro, you can see several ARM opcode that specify a certain offset within the same ELF file that changes one set of bytes whuch correspond to the values in HEX of the main alphabet Font in EarthBound into a new set of bytes, successfully making it an on-the-fly patch.

