It's very hard to say without having it in front of you. I don't know how the neck joint is constructed and what bits overhang other bits. Some of the gaps may disappear once the neck is firmly clamped together when being glued, so its' worth seeing whet that looks like with clamps and no glue.
This is the point where I'd get some chalk, wipe it on either the pocket of the heel, put the neck in and see where it's touching. If the neck isn't sitting flat against the bottom of the pocket, then sand down areas the chalk has left its mark. But if there are bits of the top of the neck joint that prevent the neck sitting lower, then they need to be sanded down.
The neck may be able to be pushed back more, but that may depend on how the end of the neck interacts with the neck pickup rout. You want the end of the neck sitting 0.5 to 1mm clear of the pickup rout, so the pickup ring will cover the end of the rout. If it sticks in to the pickup rout, then you'll have a visible gap which means that you'll either need to sand the end of the neck back, or cut.file a section out of the pickup ring so it will fit without any gap showing.
It's hard to get a totally gap-free neck joint, so some amount of filling and touching up around the joint is expected. At least you've got a nice solid colour that will hide any filler.