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What are the holes in the bottom of the bases for (flip it over)? I've noticed them on other things to.

Many of the older metal models larger than standard infantry would have a peg or pin under a foot or two so the model could be affixed securely to the base. The stands have remained even after the shift to more plastic models.

The plugs are still used on some modern models too - the Helbrute from the DV set uses it for example.

GW's "Pinning" basically. Outside metal its rarely used anymore, i usually clip them off with a pair of wire clippers so i can more easily add weight down there, since most of my models (especially ork ones) tend to lean somewhere lol.

Only metal model i have that doesnt have the slits method is my Ghazzy model. And quite frankly its annoying to base with that thing in there lol, and since its metal removing it isnt easy. Managed to hide it by cutting a larger hole in the cork plates i was using to base it fortunately.
Resin one "had" it since its the same mold but i clipped that damn thing off immediately lol

If you simply want to remove the slotta tab or nodule from a metal model, use clippers, will take all of 5 seconds to remove and then just clean it up with a knife.