Regarding the "no bouncing around" shuttlecraft.
One of the things I tried to address were the extendable landing pads, both the front pair and the aft one. In scaling up the exterior to its present size I was mindful of the step-up height for ease of entry and exit.
Now when you look at successive Trek shuttle designs they dispensed with the extendable landing gear in favour of touch points or the entire nacelle serving as a landing pad. I did something similar with my enhanced shuttlecraft design by having slim rails running the length of the nacelles much like a helicopter setup.
I really can't think of a rationale for the TOS landing gear other than it looks interesting. Well, perhaps it makes it easier to land on uneven terrain. Otherwise it doesn't help anything since they're pads and not wheels to move the craft around in the hangar area.
At any rate you could also consider that the craft could settle down fully onto its nacelles after landing and powering down for storage, or even on a planet surface for that matter. That would gain you a few extra inches.