it should be a fairly simple and inexpensive job to modify thye ankle area of a boot to accomodate a prominant bone, ask the shop if they can stretch the shell in that area, if they can't then buy elsewhere, the most important things are A) that the foot is well supported in the boot, this will minimize the movement of the ankle and reduce any rubbing and B) the fit of the boot is as close as possible without actual pain so that it is still held when the accomodation is made for the ankle bone
good luck getting it sorted out
