I did consider auto-changing dice faces, but couldn't come up with a way that didn't "interfere" with players handling the dice.
There is a global flag - onPlayerTurn only fires after the scripted setup is complete. The error seems to occur when reloading the mod an action which annoyingly causes onPlayerTurn to fire.

Perhaps you can instead set the dice in the columns to the 'supply' face when players pass the turn, similar to the way workers on research spaces become arranged?

onPlayerTurn should be limited by a flag that checks that some small amount of time has passed after onLoad. Since you say onPlayerTurn already checks that setup is complete, onPlayerTurn may need both - check that setup is complete AND skip if triggered immediately upon onLoad. This will prevent executing onPlayerTurn after rewinds and loading saved games.

Neither of these are very important... just minor suggestions for extra polishing, since I enjoy the mod.

My trouble is that I've seen a lot of players either do production while passing (for speed) or put them in the wrong place and only realise because the cubes haven't yet been turned to supply. The few bits of minor housekeeping I automated are only for things players will no longer interact with regularly.

From what I remember when I looked into it, it's not that simple. I can't even tell why onPlayerTurn is even being triggered when turn isn't changing (e.g. when reloading a single player game which doesn't have turns). It could easily be a TTS bug/unintended behaviour.