I have only tried a Reverend, so no longer term experience but I do recall the pickups be very square, like you say.
If this was me, there would be three options:
Take a file/sandpaper and very gradually file the edges of where you play the most to get it to a point where it isn't bothering you.
Get a zero-mod style thumb rest
Return it and go back to the drawing board.
It is a bit unfortunate that the one of the big pros of Reverend is their in-house pickups, so you don't really want to change them out.
Hopefully this helps and you find a solution rather than having to return a bass you like 95% of.