I'm going to let better body men than I answer these questions -- but I would say on the area being "proud" (high) after hammer welding is because you stretched the panel too much. You don't have to pound the weld perfectly flat to save yourself a lot of work with the grinder. 3 pounds of shizzaz in a 1 pound can. When you're fit up is really tight - you weld - you hammer flat - the metal that is hammered flat is going to GROW not shrink.
Ever heard of a shrinking hammer? They work if you know how to use 'em.
Hammer and dolly work is a black magic art form... I've seen people take a perfectly good panel and RUIN it because they just think you pick up and hammer and start banging away. They stretch the metal - leave hammer marks all over and then start trying to shrink it when they should have just left it alone! LOL
If you "pull" this area out with a stud gun - you'll then most likely end up with an oil can.
Ever heard of Bondo? Works real well on low areas... don't be afraid to use it.
Personally - I'd prefer a low area over a proud one.
Not sure what the right answer is on the "can't get there to work the area"... I'm all for "do my best and skim coat it".
My first job ever was at Gateway Body and Fender... back when we brazed panels on. And we did lead work. My boss was always trying to teach me his art... and a "dent" in his mind was not a dent -- it was stretched metal. His job was to "shrink" the stretched metal back to it's original shape. He'd pick up a dolly and hammer and you could actually watch the metal coming back to the original panel shape in an area he wasn't even hammering on! He's hammering here and the metal over there was coming into shape. He did this with very little effort and just the feel of constantly using his hand on the panel. I never did pick up his gift for this. It's still a mystery to me.