If the wheel isn't sitting flat on the mounting suface of the drum/disc, getting a puncture in the future is the least of your worries!
Be careful if you are filing the bore of wheels to make sure that you file a clearance to the spigot all the way round - make the hole larger than the spigot. That way you can ensure that you are not centering the wheels eccentricly. Wheel fixings with taper/radius seats are perfectly capable of centering on the nuts/bolts without center location just make sure you tighten up opposites gradually and in sequence. You only have to use centre location when the fixings are not doing the job as well. Of course a belt and braces approach is not wrong, just not 100% necessasary.