FAR makes a voxel model of the whole craft which it uses to work out drag. That means that the vast majority of parts that aren't wings will work fine. There are sometimes problems with unusual parts. Wings and control surfaces are handled differently, and they do need FAR configs to work properly. FAR is not aimed at changing the heating, though blatant bugs exist; Ferram discussed them above. FAR offers a lot more control than stock, but you can't pick an airfoil, it just uses a single generic one all the time. I'm not sure exactly how FAR works under the hood, but I'm pretty sure it's not CFD, that would be way too processor-intensive. The lift curve you show, with a hysteresis effect, is something I've seen in FAR. Many of your other questions I've never actually tested.