Tubing selection, butting, geometry tweaks, etc. And that's before you get to the utility and aesthetic matters.
Yes. The consumer generally signs-off on the blueprint.
The design is finalized through discussion with the consumer and sometimes a form they fill out. Some guys (like Bob Ross above) prefer to work directly with the builder and those conversations take place with the man who holds the torch. Others, like the OP, prefer to work through middleman/LBSs. The conversation takes place at that level.
You should never sign-off on the blueprint until satisfied that it reflects the results of those conversations.
Miles and miles of riding.
+1 to all TSL has said.
Just with tube selection alone you're looking at diameter, gage, special shaping, etc.
I've got some really, really nice road bikes, all fitted correctly. But the custom built one suits me better, in that, it does what I asked the builders to make it do. After over 1500 miles with it (only got it late last fall), I can say going the custom route really did make a positive difference for me. I'll concede I could have "made do" with something else, but if I could swing getting what I really want, why "make do"?
The key is picking really good builders, knowing just what you want, and being able to convey this to the builder(s). If I had the experience that abqhudson had, I'd be very unhappy.