Yes, I think this issue gets missed a lot, which is a shame because it's a fairly easy problem to manage and should, I think, be the starting point of a boot fit. Closely related to Noodler's next to last post.
I'll make a footbed (always as low profile as possible), trim its outline to fit the shell and the liner volume, create the under-support and deck the boot board to mate with the footbed's flat base, then start to work on the shells. I put a temporary shim insert of bontex the same thickness as the liner sole between the footbed and boot board to raise the footbed to its final height, then start locating punches and moving the shell as required. This seems to work well to adjust for what Noodler described. Rarely, I've had to make a footbed taller; mostly it's good with the low-profile design, thin-soled liners, and accurately located punches.
A P/S Media Album of my footbed build is here:
https://www.pugski.com/threads/cuff-alignment.6164/page-3#post-254138
You can't just make a footbed fit a foot sole and call it good. All the parts have to fit with one another
and the foot. Depending on the shells and the feet, it can take more or less fussing, but when it's right, it can be kind of miraculous. Nothing beats the look on the face of a skier who has struggled with foot pain when they can ski hard in a comfortable, high-performing boot for the first time.