You could put 500K pots in all three locations. You're right that would be the "standard" logic. If you do use the 250K pot, I don't think it will make much difference. I think the tone pot is not even in the circuit until you turn the knob. It would be a bit darker a bit quicker, but that might be good on a Beatle bass.
Höfner uses 250K pots on the volume as well, which would take off some of the top end, and Gibson and Fender also often use 250K or 300K with on the volume pots with basses even with humbuckers. I think it's probably one reason their basses tend to sound darker and "thumpier."
On the other hand, you have both pickups relatively close to the neck, which is a bit of a darker sound already... So the 500K pots may be a good choice.
Not sure if I am helping... I sort of use the "take your best guess, and if you don't like it change it" approach.







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