If he wasn't participating during the kitchen design and he based his price on "Set new cabinets and plywood tops. (cabinets provided by others)” without mentioning of specific items like crown molding, handles, etc he has the right to charge extra for the additional work, not to mention crown is specialty work and there is always an extra charge for that.

As kitchen handles go if you have basic one hole handles its not a big deal to put them in, but it involves extra time, some will charge for that. some will just throw that in... but in some cases, there is an extra charge to install certain types of handles.

On the general note, I have been there a few times myself... You hired to do "installation only" and during the initial meeting everything is a basic install and you price something out based on the details you been given, and you don't hear anything until you called to do the job. When you get there the scope of work "magically doubled", like in one case there was a (6) cabinet island that was never mentioned before, you have decorative end-panels, wrap-around decorative kick molding, light rail molding, etc now the so-called original basic install turned into a custom job and customer expected to do everything for the same price.

That said, if he did a good job and you happy with the workmanship, pay the contractor and enjoy the kitchen.

Good luck

Of course it’s extra. It was an estimate, not a hard price. If you didn’t furnish the proper documentation with item lists, elevations, and everything else, then thers going to be lots of add on fees. That’s what happens when you’re doing the designing without knowing the right way to communicate with your contractor.

It’s legitimate. It’s your responsibility to clearly communicate the items that you expect him to install that are purchased by you.

"Set new cabinets and plywood tops (cabinets provided by others)" lacks the specificity required to avoid the situation you find yourself in. No details of what the installation are provided.
It's also not clear which party is providing the plywood tops nor is it clear what specific plywood type, thickness, and finish are to be installed.

Ambiguity is stuff of which change orders are made.

A better approach is to produce a set of plans and specifications which clearly document the entire scope of work to be performed under the contract. For simple project scopes, a simple sketch and some notes might do the trick. For more complicated (and expensive) projects, a professionally-produced set of plans is a good investment.