I'll be in a similar boat shortly, so i'll try to help based on my research thus far. The cabinet "frame" is 90" tall. But the Sektion legs can go from 3.5-5.5" high. So if you set them at their lowest, you should have the same 1.25" clearance on top like your other cabinets.

Or am i misunderstanding your calculations?

You won’t want to just lower the legs because your toe kick lines will be off, and then you will have to modify those. And, as Hallet&Co mentioned, the real issue is making the stock doors work. Unless you are doing third-party doors, or have an open, alcove-type space planned somewhere in the cabinet, it won’t work.

I have modified many IKEA cabinets, and while adjusting for height is definitely the easiest mod, I wouldn’t do the work for .5”.

Raise the other cabinets that .5”, instead.

Oh if you want crown around the pantry you could switch to the 80" pantry & just do a filler piece of flat panel to match the doors up to where the crown would be or install a flat piece of panel top & bottom of that gap and when it's sandwiched between the 2 tall panels it'll be a nice open box to store cookie sheets & cutting boards (top or bottom of the pantry)

If you use the Ringhult fronts, the doors can easily be shortened.

We've done this on a 21" base cab that Ikea only offers with pullouts and a door.

Hubs cut the door in half to create two 15" drawer fronts to match all other cabinetry. We installed them cut-side down and even before edge-banding, the result was a totally invisible modification, as the material that the saw-blade takes off, equals the gap needed between individual drawers anyway.

Were I to shorten a door on a tall pantry cab, I'd cut down the uppermost door, edgeband and install the door cut-side up. Nobody would ever be the wiser.

We're planning on using the Bodbyn doors, so I don't think cutting them will be nearly as easy. I think that if we decide to go the route that requires a door modification we would just order from semihandmade and get everything made to the size we need. We don't have someone coming out to measure and finalize design until April, so we have some time to think on it. In store, they wanted me to use all 30 inch cabinets, so I don't want to have to rely 100% on their input. With the 30 inch cabinets, I'll have an 11 inch gap. It seems weird to me to take out our ugly soffit just to essentially put another one in. If we do go the 80 inch cabinet route, will it look ok to have the big gap there and not on the other cabinets? What do you think about the 30 vs 40 sizing?

Your measurements just don’t work with Ikea’s limitations. You should look at some other brands. Merillat basics just released a gray shaker door in thermofoil that’s better quality than IKEA thermofoil, and already assembled too. With 36”H uppers available and a whole lot more sizes and options available than IKEA.

I would do the 40 inch cabs and not do a recessed toe kick on the pantry if that allows the adjustment you need. The white bottom trim on my pantry cab is 1/4” lower than the wood toe kick...done on purpose for white meeting the dark.

I think the proportions of upper trim here look fine, but I would make it the same throughout the kitchen.

I’ve done plenty of kitchens in Woodstar that were quite price competitive with Ikea. It’s a limited choice size stock line, but not as limited in sizes as Ikea. The color offerings are limited, but they do have a white shaker in both paint and thermofoil. They come assembled and ready to install. I’ve also used Wolf Classic and it’s price competitive as well. Aristokraft has more color and style options than either, but it’s a bit more. It might be worth if you want a cherry accent for an island or some other feature. The others don’t handle cherry.

With such tight clearances, you should also plan exactly how you would install a cabinet of that height. If you assemble it on the floor, there may not be clearance to tilt it to vertical, especially with the legs installed. I'd probably build a separate base like EAC recommended above. You can then tilt up the cabinet, and lift it vertically and slide onto the pre-installed base plinth.

I haven't done the math for your cabinet and ceiling, but this image I found on the web illustrates the issue.