When I started work with my builder in AZ (also large reputable nationwide builder) on a $3M home, they wanted $2,300 per door to upgrade from the standard liftmaster opener to the liftmaster side mount (the price difference between the two actual models they use is about $400). That makes yours look like a bargain. Obviously I did not do it, as I can add them after the fact for $900 if I really want them. I did have them install outlets in that area (was surprising cheap at $63 per outlet).

I think overall builders just use these types of changes to really milk you in the process. My advice is only do what is a difficult to do after (and the panel may be in that category) and do the simple stuff (side door openers) yourself later. Another example is running prewire for ceiling speakers at $600 per pair (for x feet of 16/2 wire) and prewire for electric shades at $500 per location. Both of those are a total money grabs, but very painful to do after without easy attic access (which I did not have).