Got my answer from the discord so I'll post it here in case anyone comes across it.

PAL is generally the same and there's (arguably) no level where NTSC is advantaged, so it doesn't matter all that much.

Play in 60hz as the 50hz mode is just 60hz but with skipped frames. There isn't any time conversion like in MK64.

Are there any levels on which PAL is the preferred version? Also, if you're running the game in the 50hz mode, does the in game timer also slow down or keep going at the same speed?

The reason I'm asking is that I can play both, and I know that for some of the mario karts the slower framerate can be an advantage.

I think the leaderboards should be separated along VC and N64 lines because VC is a faster piece of hardware that has lower lag overall. I don't think it's a huge deal considering the length of the IL's, but for consistency's sake I think they should be ranked on separate boards.

The different versions, though, I think should be ranked all on one. Much like the NTSC, NTSC-J, and PAL versions of SM64 and Goldeneye are all on the same leaderboard while players are allowed to use any version they want.

Overall, though, I don't think this is that big of an issue. The practical effect this will have on the leaderboards is not that big considering that NA N64 is the most popular.

(Be warned, I only occasionally run this game)

I think there should be separate leaderboards for VC and N64, with the necessary divisions within those categories. If it were up to me I'd say have all the N64 together on one leaderboard and all of VC on one leaderboard, but if that's unpopular then that shouldn't be the way forward.

Just go ahead and delete the SRC Goldeneye leaderboards, nothing of value will be lost.