Now that the seasons are changing, I think it's time to report on how the sealant fix went on the bonus room. On average it improved the ~4 height temperature to within 3 degrees of the thermostat, and the floor improved by about 5 degrees. It was still colder in the winter, but that's in part to the unconditioned garage space underneath it. I'm not sure if more insulation would have helped further, but since it is improved (for now) we'll have to see if the sealant holds up through the seasons, or if settling breaks all of that open again.
We also fired up the A/C for the first time, so far so good. I need to get a garden hose (or 2 or 3...) to hook up to the external faucets to verify they actually work.
As for the drywall, settling cracks are coming into their own. Our bonus bath has a few, as well as a couple of the other bedrooms. It's to be expected, however I'm wondering how large they need to be to warrant a separate call out vs. the 10 month "we'll fix the settlement drywall issues" call.
With the warm weather we're also finding a few of the doors now stick, which with a winter closing and how materials expand in the heat, makes a lot of sense.