The podiatrist has a degree that says he knows a lot about feet. The fitter may just be someone who went into business for himself, and your experience with him has been rather poor.
Given a choice, I know who I would trust. First the podiatrist. But maybe most of all, me. My feet, and I know what I feel, and I'm not afraid to play around until something works.
It is so easy to trace the insole on a piece of cardboard or thin leather, or a thin dollar store insole, cut it out to create a new insole, and experiment by adding tape or adhesive foam to the underside in strategic places, until your foot is comfortable, that I don't understand why everyone doesn't do this, not just for skate boots, but for ordinary shoes. It just takes a few minutes to do each experiment. There are similar things you can do along side the foot if there is anywhere the boot is too big - though heat molding can fix many of those problems. (For some ideas, take a look the web page in my signature, in the sub-page on modifying boots.)
Once you've got the bottom surface right, maybe re-heat mold the boot to get the side and top right. You yourself posted Riedell's web page on the approximate temperatures to use, and you could do it with a hair drier. You take the parts of the boot you need to change to the temperature it is just pliable enough to form, and you form it. (Not too hot! - or you will melt the threads and glues that hold the boot together, or scorch the leather.)
The podiatrist could create an insole to do this too, and he has a lot of knowledge and experience to guide him, so maybe it takes him a few minutes to get the best possible result instead of an hour or so, but he charges a lot, and if things change, it's good and fun to do it yourself. And the podiatrist may lack experience with heat molding. (On the other hand, there must be many things a podiatrist is trained to know and diagnose that the rest of us can't possibly guess at. They spend a LOT of time training.)
I have trouble convincing most people they can help themselves this way. But you are a scientific researcher, in medicine at that. Trial and error - the experimental approach - is a big part of research. Try it! (I don't have the benefit of your medical training; trial and error, is all that I've got.)
It may or may not be relevant, but there is a difference between an ordinary podiatrist (incidentally, like you, a doctor but not an MD) and a sports podiatrist who has lots of experience with other skaters. Skates have high heals, but skate boots have much better ankle support than high heel fashion shoes, many of which have none. Many ladies on this board have claimed high heel fashion shoes don't feel at all the same as skates.
Besides, a high heel does more than one thing, if you try to analyze what you feel. On my foot, it tilts the whole foot forwards, but it also bends the foot more at the arch, stretches various muscles and ligaments, and alters the shape of and forces on the arches of the foot(Some books claim each foot has 5 structural arches that support the foot and cushion impacts: 3 longitudinal [1 on the lateral side, 1 medial -which may the be the one you meant, and another in between; and two lateral arches, across the center, and across the toes.), and possibly the bursae.
Analyze your pain yourself. Is the pain immediate, as soon as you put the foot in the boot or set your weight on it? Then maybe you are over-stretching a muscle or ligament (or more than one). (Or putting too much force on a bursa??) If not, maybe you are over-using a muscle (or more than one) to compensate for an unsupported part of your foot, or there is a point on the foot that slides, externally or internally, or has too much pressure. There are a finite number of possibilities. With your knowledge, you can probably figure it out. (Or maybe a slightly over-stretched muscle or ligament will finish stretching and the problem will go away, but don't count on it, because skating sometimes puts a lot of extra force on it.)
But if after a day or two you can't figure it out, call Riedell and see what they can do. Like any custom shoe maker, they do this stuff day in, day out, every day, and if you go to them, as expensive as the travel is, they can likely help.