Personal opinion, I like the ladder style better. It gives more track space but less scenic space. Since this is under the upper level the loss of scenic space should not be a problem. I am always short of yard space when I operate.
Regarding layout height as I commented before it is a personal preference item. My layout's main structure level is 39" The rail is then 40" to 41" high due to the scenery and roadbed thickness. Rail height is what determines how your trains appear to your eye. The 6' long section that holds the river and bridge crossings is 35" high. My highest level of track is 52", top of scenery is 68" and top of backdrop is 80". The layout seems higher to the eye than it really is because so much detail is above eye level. Either 36"/18" or 40"/15" will work. Were this my layout I would use 38"/16". Reason is based on my living with my own layout for two years. The O gauge trains are taller and the track height is much higher than my scale profile S gauge track. I would also consider supporting the upper reverse loop sections on thin posts to eliminate the 1"x3" framing on those layout sections.
I think you have the start of a great layout here.
