Consider narrowing/halving your pantry/closet and putting half on one side of the fridge and a countertop on the other rather than putting the heat from the ovens next to the refrigerator ... likely making in run more, use more electricity, cost more and potentially not lasting as long.

Why are you settling? Why not look for another cabinet line that meets more of your needs? Is this cabinet shop actually making the cabinets or are they purchasing from a manufacturer?

The reason I asked was that there are quite a few cabinet manufacturers (not custom) that have the ability to make some alterations to their lines. So onto your question. Have you asked the designer if you are able to purchase matching paint /stain from the source? Otherwise, I think you have to look at your 3 choices that you have listed and decide which ones are the lesser of the evil for you to live with.

(I guess this is option #4) I considered solving the issue by putting my "toasters garage" to the left of the sink. It would still leave me about 24" of countertop between the garage and the sink. But I don't like how it destroys the symmetry of the the uppers around the sink. (Again, bear in mind this ikea rendering is not precise...it's just the closest I could get - or the closest I had the patience to get lol)
Perhaps it would be less visually unappealing in person/practice? lol

Thanks tedbixby! Yes, so far this is the only alteration they haven't been able to make... I've had several other changes that they are able to make, in terms of changing sizes, heights, etc of standard cabinets etc. Oh, and she said they could include a quart of paint so that I can take it to the paint store for matching. This is the first real snag I've hit with customizations I want to make. I'm going to try to mock up my 3 options to get a better visual...

Ok, so here are my choices mocked up in ikea (so it's not totally precise, but close enough to get the idea.)

Option 1: would require some DIY (which would be fine, assuming we can either order the doors... I guess worst case scenario would be we order two entire cabinets and he takes them apart, but the doors have to be smaller in order to be pocket mounted. So we'd have to figure that out. So, doable, but would prefer to have the cabinet people just bring what we need and be done with it.)

Option 2: work with their garage option, regular opening doors (it would be two doors, but ikea doesn't have a 2-door 24" for the short cabinet, so you have to pretend lol)

I think this one looks the worst because of the multi-level heights. As you can see, we could do shorter in the middle, to allow a more open space at the counter, but we've still go the oven lined up directly with the garage cabinet and they will definitely be different heights.

Another option (I wanted to work in some open shelving here for decorative, not storage, but I'm not sure it's going to work. The idea was to open it up, but this just looks more closed off to me.) but we'd still have the mismatched upper oven cabinet. You can't see that in this mockup, because they have to wait for the exact specifications for the custom cabinet. But it would be taller than shown here, and thus not line up with the cabinet next to it.

Option 3: they offer the pocket garage in 30" wide and greater. I *think* they can make these taller than 18" high, but I need to double check. In this case, I'd make them line up with the oven cabinet. We'd still have the fridge cabinet at a different height, but that can't be helped in any scenario.

Option 4: put the toaster garage to the left of the sink (throwing off the symmetry around that window) and only have a garage for the family command center on the fridge wall.

Any input?

I forgot option 5. Only bake while wearing 6 inch stilettos :D Her original drawing, which has the cabinet above the fridge matching up with the fridge upper cabinet and the lower drawer matching up as well. But it puts the top of the ovens at about 68" (maybe even higher... can't recall for certain). I'm only 62" tall, so I really want the oven controls to be closer to my eye height.

If the uppers and lowers don't match, you could embrace the difference and paint the lower cabinets your favorite bold color and the walls a much more pale version of that color.