You are not going to hurt the bottom of the steering wheel. The bearing puller is your backer plate. That method will work unless the splines are extremely rusted. Which I doubt.
If the bearing puller is just grabbing a small lip, maybe you should loosen it and let it bear against a larger surface of the wheel bottom. I think you are worried you will chip off that lip?
As far as using the puller holes instead of a bearing puller. You say the flats interfere. That's why I said you may have to modify another nut. You can modify your existing nut by cutting clearance notches/half holes in two flats. That will not affect a socket from fitting on it later on.
Many Chevy shaft threads are 1/2-20. Which means you can use a lug nut to bear on. May allow access to the puller holes. If not, grind it down to whatever is takes. https://www.oreillyauto.com/detail/...hread-3-4-inch-hex-wheel-nut/dag0/611154
