So I'm in the process of sanding out the neck pocket for my neck, and it's not a "seamless" fit, and I don't think it will be. (seems like the top of the pocket flares out a bit)

Is this an issue besides cosmetics? Is there anything I can put in the gap that will look better than nothing? I'm finishing the wood in just a gloss finish, so it's pretty light.
give us some picture. Also, you need to make sure that your sanding does not result in the neck pocket shifting to one side if you have already drilled the holes for your bridge.
A little room in the neck pocket allows a bit of adjustment of the neck side to side to align the strings to the center of the neck if the bridge and neck isn't lined up just right.