good questions Andy, I presume the half circle in the neck heel is the way the router bit has cut all the way across to get a square edge.
Question 2, you really need to see if you can remove the inlay that is a bit too low. You will risk breaking the inlay so may be up for a new one. Never seen this problem on a G type neck.
The slightly higher binding won't be a problem when the neck is glued in place, as long as the neck heel is making full contact with the bottom of the neck pocket should be fine. If the binding is preventing this then sand or cut the binding flush.
Thats right karijini, all these build diaries hard to remember all the info !