We have 5.5 inch crown, it isn’t too much at all, looks very nice. We luckily were able to match it to the existing crown we had in our family room/kitchen, but it looks seamless. We also have 9 foot ceilings and stacked cabinets.

but contractor is telling us that is our only option unless we get a customize size cabinet.

I am a little confused about the math here and why your contractor is saying custom sizes. You did not provide information on most of the measurements. I have 9' ceilings with stacked cabinets. Here are my measurements:

Floor to top of counters = 36"

Distance from counters to bottom of upper cabinets = 18"

First row of upper cabinets = 36" tall

Top stack of upper cabinets = 15" tall

Crown = 3"

Many people get 6" crown. I wanted a smaller crown, with a 15" upper stack. Just my preference. None of the sizes were custom. If I had to do a new kitchen, I might make the upper stack a bit taller than 15" and the lower stack a bit shorter than 36", because I have seen that proportion on this forum and like it. But I would keep the crown at 3", which I prefer, but many people like a bigger crown, so it's personal taste.

We also have 9' ceilings and used the same 6" high profile throughout the kitchen and family room for a seamless look. Our local lumber yard matched the profile of the painted crown that came with the cabinets for less money and our painters finished it. I am afraid that using stops would look like you didn't have an experienced trim carpenter. No matter what size you choose, I would make it all the same.

So more information ours is the same as yours...

Floor to counter- 36 in
Counters to bottom of lower wall cabinets- 18 in
Counter to ceiling- 72in

We are using Omega. He is insisting we need custom upper to use 3in molding.

Cabinets- total 51 (he says Omega doesn’t make lower and uppers in this size std)
Trim- 3
Counter to cabinet- 18

I'm sure Omega has pre-made stacked wall cabinets. Most semi-custom and custom cabinet brands now offer this. No one really 'stacks' anymore unless you go with a brand that doesn't offer it.

To fill the space above, You can do a flat stock molding + crown molding ....so then you can go with a crown that's similar or same height as the existing room crown.

Have you ordered your cabinets yet? Sounds like this needs some more planning and thought.

Off topic: Your last name is similar to my maiden name which is Osvath. I have a Hungarian family tree that dates back to 1616 with the original name written on it as Osvald. Just thought that was interesting and I'm totally a genealogy nerd.

Mystery solved...sorta. Kitchen guy just told me after dealing with him for 2 months, not stacked cabinets but one transom cabinet. Omega only offers these cabinets in 3 sizes and unfortunately the top section can only be customized to certain heights with insane up charges. He currently has our setup as :

Lower section: 33
Top section: 18

To change to 36 and 15 is going to be very expensive.