It always splits after you confirm the score board. However this raises one issue:

The final split won't occur right after killing the final boss. Instead you'll have to confirm the final score board to trigger the last split.

Would it be possible to change the rules to accommodate for this? It would make the run 3 ish seconds longer and we'd probably need to adjust the current times on the board though.

Can I still use the auto splitter even if the rules won't be changed? I could just read the time on final hit from the video.

From the rules: "The only allowed emulator is the latest release of GambatteSpeedrun (Currently r614) with a GBC bios image. All other emulators are banned."

The old patch is faster because faith (gear) has 696 stats. They nerfed it down to 333 stats on current patch.

I think most people just happened to own it on PC. The NG+ and eventually Mew Game categories are current patch only (because these modes don't exist on old patch) We also just recently started experimenting with new categories. NG+ and 100% seemed obvios but Mew Game has potential too. All dungeons was also suggested.

Some people tried it on switch and it seems that zips don't work on it.

I usually just delete the older submission if it wasn't accepted yet and submit the new time afterwards.

You could also use a smartphone / tablet with a stopwatch to time the run.