@ Chris--that's a great summary--maybe it should be a sticky below Bud's original information.
@ Matt--Many thanks your contributions here and elsewhere. I always learn something.
I have problem feet: collapsed arches, big bunions, chronic pain, Morton's neuroma surgery on one foot, lots of rehab to manage the same pain on the other foot. In my life (49 yrs old) I've tried dozens of insoles, from very expensive insoles made by doctors, to things like Superfeet, to cheap stock insoles. It's really hard to know what will work, and spending loads of money, or going to the people with the best reputation, is absolutely no guarantee of comfort. In this respect my general criticism of the custom insole world is somewhat similar to the criticisms directed at the ski boot world above: it's as much art as science, there are diverse and widely divergent views, there is no one right answer, everybody has to find what works for them, and that might just be what intuitively feels most comfortable, despite what the experts say.
Regarding insoles in ski boots, I did post here last year about the differences between insoles for walking vs insoles for skiing. The general consensus seemed to be that 1) insoles for walking are designed for that purpose (obviously) while insoles for skiing are designed to support the foot and apply pressure to the inside edge, 2) Despite the specific nature of ski insoles, if one has custom insoles for walking it might be a good idea to try them in ski boots, and 3) insoles will definitely change the fit and feel of ski boots.
Having been to a few boot fitters, some wanted to mold with custom insoles inside (their insoles or mine) some refused to mold with insoles inside for fear of destroying them (again, their insoles or mine), and some wanted to mold without insolves, and then insert them afterward, to make up for some natural packing out of the liners. I can see merit in all approaches, but, if the molding and shell fit process is really so specific, it seems that the only way a proper liner and shell fit could be achieved is with insoles in place. Otherwise, everything would change when you inserted the insoles, as you said.
But, let's pretend you make a custom insole, mold a liner and shell with that insole, and then perform all the fore/aft and lateral adjustments described above. Couldn't an argument be made that it might make sense to mold the liner and shell again at the end? Sort of a "final mold." Afterall, if you insert heel lifts, change lean angles, add shims under bindings, and so on, you are going to change all the pressures and forces in the boots. I can see how this would easily create pressure points, empty spaces, etc. Maybe you'd have to do the whole process, over and over, in a series of iterative steps with changes of diminishing magnitude until you converged on boot fit nirvana....God, it's too much...let's go skiing!