I like the way you are approaching your build. Lots of good thinking, good questions. Below are some thoughts from decades of building layouts that may be of value. When designing the build of your bench work there are a few determining features which you may want to consider:
Consider extending your grade as far back to the overpass as possible.
The over under point is like a corner stone, the point from which all dimensions are referenced.
A 2% grade of tangent track and a 2% curved track have different resistance values.
A 2% 054 curve and a 2% 072 have different resistance values.
Consider using a single piece of non rigid 1/2" plywood to form your vertical curve easement allowing at lease 8" of flat at each end.
3' 4" piece of 1/2" plywood would provide a 8" flat, 24" of actual vertical curve transition and 8" of flat. Personally I use 36" of actual vertical curve transition + 8" & + 8", 52" overall. Your mileage may vary.
As Rich says 42" is a very common layout height. One thing I used to do was to set some 38" high, 42" high and 46" high 2' X 4' "tables" up in a customers train room with instructions to work on some projects to find a comfortable height. We all have different heights, leg lengths, torso lengths, and arm reach. You must be comfortable to be enjoyable.
If you always have to use multiple power units or if you always have to get a running start to get up a grade, that can get old.
Using a thin bottomed overpass bridge could require less rise.
Excluding certain types of rolling stock could require less rise.
Use of a degree gauge, (Micro Mart) a plumbers level or a short level with a incline spacer can help you to develop a consistent grade.
Craftsman 4' level #39255 has incline markings for ease of ramp building.
The loop around your" whatever scenery"...if you could send your spouse away for a 3 day weekend consider running your loop through the wall adjacent to the door frame then curve up the sketch and return through the wall at the tunnel portal and you will then pick up several additional feet of overall grade length.
Try not to think of walls as a boundary but rather a reference point, simply a datum line. The only real wall restrictions are in the stud, electrical and havc ducting category.
Just because all your legs are cut to the same length does not mean your benchwork is level. Assuming that the floor is level can be misleading. What are the first three letters of assume?
360 degree laser levels are reasonable priced these days. I use a Delta.
8' levels can be very helpful. Use levels in pairs or quad to speed up the leveling process.
I am sure there are some points I have over looked.