Each FZX player has a personal setting which says whether they submit times as PAL or NTSC. I think our best bet for FZX separation is to check that setting. There has also been discussion (e.g. on Discord) of separating the F-Zero SNES ladder into NTSC and PAL though, and if we do that, the only things we can go on are the country flags. (EDIT: Uh, I actually didn't realize SNES had NTSC/PAL conversion on FZC too, so scratch that!)
And yes, rankings and forum accounts/content would definitely be migrated over.
The current site's ranking and forum integration may have its advantages, but I think the biggest problem is that we have a lot of forum-software modifications which make the forum software really hard to upgrade. You can check out the "Announcement: Developer log" thread in this forum for more technical info on the upcoming site upgrade, planned primarily by me and locks.