You can attack it from a couple of different angles... If the crown is all the same, then you can consider it all "room crown", and you can then paint it all creamy white. I have seen instances where the crown is all the same and the color simply transitions to blue at the soffit-to-cabinet crown miters. Your choice. I prefer to make the two crowns different though, making the cabinet crown smaller than the room crown. With the cabinet crown minor to the more major room crown, cope the cabinet crown to butt into the room crown. Paint the room crown white and the cabinet crown blue. Much depends on the size and styles of the crowns, etc, how they meet up, how they relate, etc. But it really boils down to your personal preference. The good news? It's only paint. Easy to change if you decide to change your mind.

the biggest problem with crown on a vault, is not on the vault part, or even against the flat part on the second level, because both of these ceilings are 90 degrees to the wall. The problem lies at the bottom of the wall, where the crown cannot make up the height difference of the pitch of the ceiling. It will take a plinth block of sorts in the corner to make up the differential height, and even then, the bottom piece of crown will not intersect the sloped ceiling correctly.

There are two fixes I see at this point: Hold the crown down so that it reads closer to level which will result in a gap at the ceiling and then "float" the ceiling with compound. In concert with this you can also likely back plane the crown to help "bend it" and that will help. You will likely still see it but it'll be an improvement. It is a known technique to address this issue. Your guy should know how to do it. Second option - rip it out - rip out the sheetrock and shoot the ceiling joists with a laser and level it. Sounds extreme and it is at this point but it's also your house and you should be happy. Now, I completely disagree with everyone that's saying its an old house and its a remodel. It's relatively easy to get this right if you are paying attention. It always comes down to time, price, and/or quality. As the saying goes pick two. As you are the client, you set the tone. And if the tone you set is speed or price then this is not an atypical outcome. If the tone you set is quality then frankly your GC should have shot the ceiling with a laser before he rocked and hung the cans and got a sense for how much he was out. Then told you, perhaps showed you with the laser and provided a price for leveling it down. Then you own the decision. Frankly, that's our standard operating procedure - primarily because you hired our firm and we do it once and we do it right. but also because I don't want the call and I certainly don't want you unhappy. But there are levels of contractors and it also assumes that you have sent the signals that you care about quality. If you are at them to finish and they are relatively on schedule then you are culpable as you set the tone. Is he on a bid and did you go low or push for him to catch the low bid ? Do you want it right or do you want it right now ? But if you were all about quality and paying a fair wage then it's all on him. You have to decide what you can live with it and where you are budget wise. I'd have to see the rest of the kitchen to make the determination as to the preferred course of action. But as we like to say Do it Right and Do It Once so I think you should talk with GC and come to some arrangement to at least try to remediate the problem. Heck, it's right in the kitchen and the job has his name on it. And don't be cutting any checks until you have the conversation.

ffjunk, of course it's a personal choice, but thought I should add, we have a situation similar to yours, with a pass-through window between painted cabinets, as well as a pocket door between a cabinet and a cabinet pantry. Our cabinet crown molding, and our whole house crown molding are the same heights, but different cuts, so the choice was easier for us - keep the same crown molding throughout the kitchen, though it is open concept. We are using stop blocks at the pocket door crown as the pantry is a stained along with the crown molding above it, and the cabinet adjacent is painted, along with the crown above that. The trim around the door will be painted the same as the cabinet/cabinet crown molding. Our ceilings are 9'. We are also using a stop block where the whole house crown meets the kitchen cabinetry crown - it would be very difficult to both cope and scribe the crowns to match and we prefer the stop blocks. I don't have photos as we are still in the midst of remodeling and our cabinet maker has yet to bring and install the stop blocks.