There are two different versions of Super Mario Collection (JPN) that I can find for download: a regular one and one that says "Rev A". Is there any difference when it comes to speedrunning the games?

You'd probably want the one that's not Rev A. One difference I'm pretty sure is in SMB2-US, you can do quick pauses to try to skip the freezing of the characters until the door appears when you kill a boss. I feel like there may be some other notable differences, but that's the only one I can think of right now.

For SMB1 there is no difference between "regular" and "Rev A" (or "1.0" and "1.1"). You do want the Japanese version however, because the flagpole sometimes drop you off faster.