The entire purpose of boot-fitting is to get you into a boot that skis well and is comfortable. Do whatever it takes to get there.
That might mean the boot feels great from the start and you don't do anything to it: you love the out-of-the-box fit and that's awesome. In this case, don't touch the boot. You already won.
But, if something needs a little love or you just want to get the most out of the fit of your boot, there is no problem with heat molding a liner before you ski it. It will not degrade or weaken the boot in any way (provide it is done properly). In fact, some liners deserve to be heat molded before you ski them. There is no point in buying an Intuition liner or especially a Mimic liner and not heat molding it before skiing it. Simply skiing these types of liners will not cause them to sufficiently mold to you, they need to be heat molded.
This is especially true if you are feeling pain in the boot before you ski it. In this day & age, there is no need to suffer in order to get your boots to fit well and ski well. If you have a problem, you should address it before skiing it.
If your foot is wider than the shell, then no amount of skiing the boot will make it feel good. You cannot make the shell wider by simply skiing it; you will need to modify the shell in order to be comfortable.
A good boot-fitter will absolutely notice any red flags before you ski the boot. Always take care of a red flag before you go out.
TL/DR:
1. If the boot feels awesome, don't touch it.
2. If the shell is a good shape for your foot, but you want it make it even better, then heat mold the liner.
3. If the shell is too narrow for your foot, then expand it where necessary.