First off, you're going to get much better responses in Gear Talk about this.
Secondly, there is no universal rule that all shops must have to do the same thing. Some do not charge for boot-fitting labor when you buy the boots from them. Others do. It just depends on the shop. A common practice is that when you do buy the boots from the shop along with a footbed, they will offer you a boot-fit guarantee. This is more often than not a much better deal in the long run than buying online.
All shops can and should charge you boot-fitting labor if you did not purchase the boots from them. These fitting services take lots of time, training, and expensive tools so you should be prepared to pay for it just as you would any professional bike labor or car labor.
Feet and leg shape can change over the years, but generally speaking once you have stopped growing you won't have super major changes unless you are involved in an injury.
This is by no means an exhaustive list, and there are plenty of great shops not on this site, but check out: http://www.bootfitters.com/
It will at the very least give you a starting point if no one here can point you in the best direction in your given area.