They are likely pooched out from screws,that held a rearview bracket. Find another rearview or ya could heat n pop back inword,then fill. What ever way ya like.
I've tacked a nail head in a hole like that (not pulled out though) and mig welded it in. I filled lots of holes in the Stude that way. Just tack it, then cut the nail shank off, weld and finish. Now if the hole is smaller I'd use copper as a back plate and weld it up.
If you want them even with the rest of the door (flat), you're going to need to hammer the high spots down and fill or drill them out until the hole is even with the surrounding sheetmetal, then weld up the holes. I'm guessing you can't get to the back side, so hammering them down might be tough. I'd drill them out, fill the holes, and grind things smooth.
Use a punch to tap them back in and weld them up. I know with all the expert builds that metal finish on here, I wouldn’t be above using a little filler to finish it. If your dead set on metal finish, then hole saw around raised area and make a plug.
If you only have two to fill feel damned lucky. I think that there are 58 holes drilled in my 71 GMC and around 30 of them left after I swap the doors that have about ten in each door. Both bed rails have about 10 holes in the top because every time my uncle mounted something different he drilled new holes to do it rather than drill up from inside the bed though what he was mounting. My dad bought him the damned drill for Christmas one year too boot. Since there is no way to get to the back of the holes I'd have to say that using a drill to cut the ragged pulled part off and a fat center punch to then push the raised surrounding down is probably the best go at it. I've got spots that look just like that on the bedsides on the 71 where my uncle had hooks mounted.
That area has a inward curve to it, so you’d have to get it lower than the curve, fill, then filler to match it up. If you just open the hole, make a plug, the plug will sit above the inward arc and you’ll have a high spot. So make it lower, or get creative with the plug to match to the profile. Now that’s just my view looking at it on my phone.