It is not just like the SNES version. It is just like the GBA version, exactly. It is the exact same as the GBA version. You can submit the runs on the GBA page because that's what it is.

How did you get the impression that the game was updated in any way? Virtual Console is just an emulator. Are you refering to post-processing effects like screen smoothing?

Submit to the GBA leaderboard, it doesn't make sense to compare runs of the GBA version with runs of the SNES version.