Just those two? There could be a few differences, but the most noticeable would be size ? But they also might have different ESRs, which when combined with eddies from the pickups
can cause changes in tone on the treble due to the varying impedances. And this is just skimming the surface really.
I suppose it would be the same answer for any two caps though, they are not ideal components and as much as people like to think that "if the value is the same, they will sound the same" that's just not the case. There is a possibility of it altering the tone even when the tone pot is all the way up. In some cases it will not be noticeable, in others it will - only way you can find out really is by testing for yourself.
For the technical minded...
If anyone wants, PM me.