MartianDestiny makes a good point about being comfortable with your fitter. If you are having any pain issues, a good fitter will want to know about them. Mine wanted to know what I liked/didn't like about my previous setup. If it had not been stolen he would have wanted to watch my form on the trainer.

If your fit is causing you pain or aggravating injuries, your fitter should be able to tweak things, so long as you are on a frame that is appropriate for your body. Technically, I am not on a custom frame; I would call it a stock frame made by a specialty framebuilder. With a custom paint job

I don't think bike fit is necessarily a static thing. Your ideal fit might change based on your overall health, fitness, and goals. As an example, when I was measured for my bike I had limited ROM in my hip & lower back due to an injury but I was also experiencing slow but steady improvement since I was still working with my PT.When they built the bike up initially, the fitter put me in a more upright, less aggressive position. Several months later I was ready to have the fit adjusted and all we had to do was remove a spacer.

It is now two years later and I just had the fit checked again, since my toes were feeling uncomfortable at the end of last season. Turns out one of my cleats had moved out of place. Could also explain some lower back pain I was experiencing. So he fixed that, and also adjusted my alignment and moved my saddle down and forward a tiny, tiny bit -- in theory he says that should improve the power transfer through my foot. So I'll try this out for a little bit and see how it goes.

I think it's fair to ask what you can reasonably expect from a custom fit vs. having expectations beyond that which will lead to the disappointment you speak of. Some people will talk about custom fit like it's the Holy Grail of cycling. But not everyone needs a custom frame.

When I brought up the idea of going to a custom builder, it was more because I know how frustrating it can be to play retail roulette if your body isn't in the middle of the bell curve. A shop that is building their own frames will tell you if you'll be waiting 6 weeks, 6 months or 6 years. And since they tend to be small, you can bet they will work hard to make sure you are happy with their product.