CliftonGK1

- the saddle height is too low.
Raise the saddle.

- I feel cramped, which might be from the too low saddle and my too big belly.
Could be a combination of things. First to look at would be your reach to the bars after fixing the saddle height. You might need a taller/longer stem after hiking the saddle up.

- the bike is faster than Roark, the Trek 7.5 fx I've used for touring.
By design, it will be more efficient so it will go faster for the same energy expenditure.

- my feet feel closer to the bike frame, even with extenders on the pedals. (I need extenders, since I'm severely knock-kneed.)
They might be. The cranks on the touring bike may be narrower than the cranks on Roark, even if they're both triples. If they're different pedals, that could play into the equation as well.

- the bike feels more twitchy in handling. I can't tell if it's the two week layoff from riding I've had during my knee injury, the speedier nature of the bike, or my new riding posture
Roark isn't a drop bar, IIRC. One of the things I notice going between my upright townie handlebar bike and my drop bar rando bike is the feel of the steering. The wider your handlebar and longer reach from the steerer tube, the slower your steering will feel for a bike with identical head angle, rake and trail. It's because you have to move the bars through a longer arc to attain the same degree of rotation. For me, moving from a wide upright bar to a narrower drop bar makes a huge difference in steering sensitivity.