Autoleveller

You must be using a blunt drill, bent drill, slow drill speed or far too high feed rate if your ripping up pads in all honesty.

It might help in the future to use the engraving tool to simply touch down in the middle of each pad first creating a centre for the drill to follow later.

You must be using a ...

Quite possibly any and all of those! Sometimes things aren't perfect (you forgot to mention the PCB glue) and the name of the game is making allowances for that.

Nevertheless, even if it were perfect, I think the desirability of retaining probe points should be quite high since even a single etch can require a tool change (from fine tracking to wide rub-out, for instance). Even if that's done as two jobs, as would have to be set for the holes now, the second part would need a re-probe but now there are tracks all over the place. Might as well be holes

Having thought about this, I reckon that if the leveller app could be modified to use an imported grid, it isn't necessary to deal with how that grid is derived. So long as we know the format required, anyone can get their machine to do the required stuff and, if necessary, convert that to the leveller input format.