Wax could go either way...it's likely that over the years, that which squeezed into the drain path just eroded away. I think you'll be fine with a standard wax ring.
The flange could be reset to be where it's supposed to be, but not all plumbers actually do leaded flanges any more. As long as the toilet doesn't rock, you should be okay. It it's really sitting porcelain to metal, you need to address this, or you could have a catastrophic failure.