"I'll show you a picture with the cabinet as I mean it. The microwave is behind the 'flap', directly above the stove. You can leave the flap open, and if it should look tidy, just close it."
Yes, that's how I understood it too. But still, you "lose" part of the (actually planned) tall cabinet volume.
"Next to the tall cabinet you can put in a narrow pull-out pantry cabinet. We always find it practical for baking stuff (flour, sugar, etc.) etc."
We have such a pull-out pantry cabinet (210 cm high, 30 cm wide), but after 25 years we never really got used to it.
"Why don’t you plan in a kitchen tool (you can represent the room there too) and have access to the underlying system (cabinets etc.) and when you're done you transfer it into your 3D program?"
Yes, that's what I'm doing now. But ultimately almost all installed cabinets (width, height, depth) are also available in these planners, as I created it.
"Where your shelf is now I would place a large French door refrigerator."
We had that idea of course, but we want to keep the option open to use this area (temporarily remove the shelf or maybe it won’t be placed there at all) for seating (putting in an additional narrow table; then the terrace door simply doesn’t open).
"I would also use the full height."
My wife is small, she advocates for low cabinet heights and few tall cabinets...