Because the double oven unit is stand alone and not touching other cabinets, I don't think it is a problem to have a higher toe kick there. Plus, it is right next to stairs, which have a riser height that will compliment the higher toe kick look. It will probably bother the hell out of you for the first few months just because it is not the way you intended, and then you won't even notice it. I guarantee others will not.

I was confused about the pantry piece you were talking about - where it lives and what is on either side of it if the base is higher.

HI -- Is that company scheduled to finish this ? The proper space from counter top to bottom of over cabinet is or should be 18 inches . Is there going to be under cabinet task lighting ? Is there planed to have a valance under cabinets for the task lighting . If there is less than 18 inches or a little more allowing for the size /inches of lighting valance ? What ever you do ... do not pay the last amount to this company until everything is done properly . Maybe bring in a finishing carpenter to go over the details of the correct things to do to finish this properly or ask another kitchen company for their opinion on trimming this properly . Bringing the top cabinets up higher is not what should be done unless they were set too low in the first place . To fill the space there might have to be a straight valance board and then adding the crown to the top of that or by adding a bigger deeper crown molding . Look at some similar kitchens here on Houzz to see what the top crown and finish is or what looks good to you as a reference picture . But I do think you need to talk to the company owner or another company or a finishing carpenter to see what or should be done . Please stand your ground ! Just saying raise the cabinets is not the right thing to do without looking at the problem . If that company does not want to do this the right way do NOT pay them the last amount !!

You don't "raise all the cabinets", you fill in the gap between the top cabinet and ceiling.

It looks like the upper cabinets combined should have been 3" taller.

Your Kitchen Designer should know what a Profiled Starter Molding is. It is an L shaped pice that is placed on top of the cabinets and to which you attach the crown. I would suggest running that same cabinet crown profile around the whole room. It’s what we try to do on most jobs.

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There is a reason that that cabinet seller is no longer with the company. She messed up quite a bit. And I mean a LOT. That design is not acceptable. And you are a ways from needing to be concerned about crown.

You need to invite the company owner to come to the job site and fix more than just the crown molding. Simply ask him, "Is this a kitchen that you could easily cook in?". If he says yes, he is lying. If he is honest and says no, ask him what he is going to do to make it right.