I'm thinking there might be a legitimate issue there, but the way he explains it doesn't help much. (The issue is the game uses the CPU clock as the in-game timer, which results in certain events happening 1.5x times earlier than they should, and the save slot "Game Time" value is calculated based on the current system, so swapping between Nintendont and MIOS/GameCube results in inconsistencies.)
Either way, unless someone who's really into TTYD and can reverse-engineer PowerPC code takes a look at it, it probably won't be fixed. :V