I don't *think* you will have any issues with doing it this way, though it would've been much better if he had welded pipe in between the lower frame repair and the upper frame to prevent crushing. Looking at the amount of rusted material, it looks like the welder would've had the room to do this. I would imagine these bolts will be much more likely to work loose however, so I'd keep an eyeball on them. Also, drilling holes in the frame (now you have upper and lower holes, obviously weakens it, something else to keep in mind. I wouldn't have done this, but I don't think it's the end of the world. I mean, he could've drilled holes in the new lower plate he welded on, and welded bolts pointing downward to bolt the skid on (like studs). This would've been a better approach assuming the material he welded on was heavy enough, and overlapped enough good steel where he welded it. He may have gone through the frame because he wasn't confident his repair will last.
The thing I don't understand is that if your frame is this bad at the skid, I can't believe there aren't other serious issues of rust. I mean, this is some serious rot. I'd take a hammer to all the common rust areas and hit em' a few times to see what gives. It would be extremely unlikely that the frame would've completely rusted out around the skid but not, say, at the usual rear lower control arm mount area.