stance and alignment are not independent of boot fitting. everyone, yes everyone thinks that they are.
the process as a whole includes measuring and shell sizing the foot, assessment of your ankle joint range of motion, arch flexibility, and any forefoot alignment issues, underfoot solution to match the previous assessments, cuff alignment, and finally sole cant.
based on your original questions from post #1.....
"So I was wondering if the struggle I have could be caused by a limitation in my feet?"
the answer to your first question is yes. now based on the follow up info that you have provided the solution definitely has something to do with your next statement, "I have some restricted range of motion in one of my ankles due to an old injury. I also have high arches and so when standing throughout the day I notice that it feels like a lot of my weight is naturally on my heels causing heel pain."
now to your second question......
"I already have custom footbeds. Is there a boot fitting cure that can help this and if so what direction should I go first?"
couple of points: first of all the process as a whole includes measuring and shell sizing the foot, assessment of your ankle joint range of motion, arch flexibility, and any forefoot alignment issues, underfoot solution to match the previous assessments, cuff alignment, and finally sole cant.
using your description of what is going on, the 2 most obvious places to take the closest look is closest to your foot. you say you have a footbed and that the footbed was deemed ok, i would start my sleuthing right there. based on ankle issues and arch issues i am suspicious of your footbed. as far as internal ramp and forward lean are concerned, your arch flexibity is the next important clue to getting things correct inside the boot. and related to that and in line with having balance issues, i think that you are in a boot that is too big, or not the correct match to your foots shape.
now on to the big question...."Is this issue something that can be helped via boot fitter?" the down and dirty easy answer is yes, however it will not happen if you go back to the last two guys you queried about you footbed and shell sizing. you need to find a guy that knows what kind of footbed to build for your foot structure and get you into a proper fitting and flexing boot for your unique set of circumstances. you haven't offered up where you are located, so until we know we cannot steer you towards the right boot fitter.