I use tokens to mark activated abilities, dice for totalling the current conflict strength, and in complicated conflicts additional dice to keep track of boosts like Banzai. Recently someone told me that this may not be allowed at like a Kotei on the logic that it is the same as taking notes. Reading the tournament rules it seems to me that it it's clearly talking about taking written notes. It provides rules for replacing the normal tokens, but provides no rules that I can see about anything else. Can anyone verify this one way or another?

I clearly remember seeing the players at the Worlds’ Final using dice and custom tokens, and nobody said a thing.

Yeah, you can use dice for that. But you can't use them instead of fate or honor tokens.

Although if you are using custom tokens for fate / honor an opponent is allowed to ask you to use the default paper fate / honor. This may be especially the case when fate / honor tokens can be easily mistaken or are hard to read.