OK, I went ahead and opened up my JTV-89F and took a closer look.
The volume is a 3 gang pot, with a A500K, and (2) B10K pots.
The Tone is a 2 gang pot, with a A500K, and a B10K pot.
So I would expect that the A (audio) gangs are for the magnetics and the B (log) are for the Variax (10K is a typical value for expression pedals).
So yes, they are "special" because it is not common to have mixed values in a multi-gang pot, much less the custom PC board that is used to connect to them and the interface cables.
But no, in that, they are pots, and pots are pots.