Here is the mistake he is making, he is trying to "blend" those spots in. It is as simple as pie, you don't do that. This is my point, you don't ever put the last coat of filler on, a skim coat, until you KNOW it will be the last.
You don't even try to blend those spots in, not any more that is that a skim coat over the top will cover any imperfections.
Here is my "Basics of Basics" on the subject.(Click here)
With this method you don't have to baby these low spots, you apply filler and you CUT
it flat using NICE, NEW, SHARP, QUALITY paper. This paper can be much coarser than you would use to try and "blend" it in, being it is much coarser it will CUT
it flat very quickly.
Once you have the panel flat, (as flat as needed where ONE coat of polyester putty or primer will finish it) all the lines nice and sharp, where ONE thin skim coat will finish it, you spread or spray a polyester putty on the entire area and block it to perfection. I have a guy I have worked with for ten years still calls that last skim coat of polyester putty "Primer" because of what I taught him years ago. You look at it as a primer coat to fill pin holes and sand scratches and poor feathers, that is all you are asking it to do.
This method was taught to me by a very good bodyman and I have passed it on to many guys in the shops I have worked and watched them turn from someone who fights filler to a two application mad man.