I replaced my Atomic 9.50's (from 2001?) with M10's because the shells seem to be almost identical. The 9.50 were comfortable out of the box, but my right foot felt as if it were trying to twist inside the M10, and there was pressure on the side of my little toe. Switching back to the 9.50 liner solved the problem, so I compared the liners.
The 9.50 had a hole (about the size of a quarter) cut in the plastic outer surface if the tongue, right above the bump on the top of my instep. (The bump is about halfway between my ankle and my big toe. The hole in the tongue is below the hinge, on the big toe side.) I cut a similar hole the tongue of the M10 with a single edge razor, and the fit immediately improved. I think what was happening was that there was not enough room for my extremely high instep, so my foot was pushed over onto the little toe side, creating a hot spot there.
After about 10 hours I developed a pressure point on the big toe side of my instep, lower and closer to the heel than the bump on the top of my instep, where I have a promininent bump. ( I think that is a bunion or a very large navicular bone.) The M10 liner has a plastic layer sown over the ankle bone that extends over the bump on my foot. The 9.50 doesn't have that, so that plastic peice may get the razor next, or maybe I will try a different footbed.
I think most hot spots in boots are caused by an unstable foot that rolls over until it rubs up against something. Punching out the boot doesn't always help because the foot just rolls further before it hits the shell. The better approach is to stabilize the foot with footbed. I always try first to shim under the footbed if I think my foot has developed some instability.
Hope this helps.