Arches in ppls feet also change a bit here and there depending how often someone is on the ice, whether they wear orthotics, summer time where it's mainly flip flops etc. That's why I like speed plates as well. I like how the speedplates are completely custom and I really like the hard material it's made of. I can't stand the sponginess of conventional footbeds and the true footbeds which my feet feels like it's slipping on.
I agree with you that even custom skates require additional customization. Like yourself, I also made my own version of powerfoots and reduced the height of the toecap inside dramatically where there is almost no space for my toes to wiggle.
Also, some people like their toes to brush up on the end of the toe cap, some like not to feel it at all, and some like it crammed. Maybe true should have these questions answered during the fitting so they can adjust the skates to those preferences, but realistically, those are easy mods to do yourself with some toe plugs.
Even the red insole. Some use it some don't. I personally don't use it because it gives the skates a bit too much of a padded feeling on the bottom of my feet.
At the end of the day, for those who use retail Bauer skates but go custom bauer ( or even CCM to CCM custom) will prob be happy with the fit out of box bc they know exactly what they are getting with the skate. There won't be an adjustment period on how the skate performs. Fit will only be better since it's custom version of what they're used to.
Most ppl going to trues for the first time will need to adjust no matter what bc it's a completely different skate fit and feel wise. I do realize there are fit issues that's not related to the adjustment period.