As always, more comments.
It sounds like you're leaning toward the around the room design with the 36" decking and peninsula. I think that would be a good choice and we can work on enhancing it. If that's not the case though, then I'd like to know the footprint of the pull-down ladder, both where it is in the ceiling and where it ends up on the floor. As I said, my last design option did not take that into account and might be a reason to dismiss that option altogether. Also, you gave us distances from the walls to the pony walls around the stairs, so the rectangle in the design should be close to accurate. If it's not, that's something we need to fix.
Any section can be made modular and mobile if you plan ahead. Tracks can be cut where the modules meet. The hard part is separating the landscaping, especially when you add elevations, mountains, etc. If you plan ahead, there are things you can do to keep the sections separate and not have to try cutting them after the fact. Here's a link to a thread that shows how to do a swing-out module. This is a corner module, but the same concept can apply to a pull out modules at the windows or beneath the mini splits. The module could be a simple rectangle, but a wedge might be a bit easier to get in/out. The window side would be as wide as the window while the aisle side would be a bit wider to eliminate any binding. The depth would have to be less than the width of the aisle.
https://ogrforum.com/topic/340...275#3963862654517275
As far a separate level vs continuous grades, I designed a layout with 2 completely separate levels. The owner wanted a logging operation for his Shay, but we didn't have room on the main level with all the other stuff we had there. And he didn't want to create just a small scene with a camp, a mill and a lumber yard in close proximity, he wanted a full run. So, we decided on a 2nd level for just the Shay and logging. I'm also helping with another design that also has a partial 2nd level. I'll send the SCARM files separately, so you can review the designs and 3D views at your leisure.
The problems with connected levels are the amount of space needed for the grade tracks and the amount of the main level that gets covered visually. Depending on what you want on the main level, decking that is 36" wide doesn't leave a lot of room for somewhat useless grade tracks going up/down. They take space away from operating tracks on the main level. Most multi-level designs I've seen, separate the levels by 18" for unencumbered access to and visibility of the main level. Some folks confuse the terms multi-levels (separate) and elevated levels (connected), both have multiple levels.