First of all, I do know this is not an ideal solution, but it has given me the best outcome in most cases, compared to all other approaches/tricks currently possible in darktable.
Yes, although it’s not a big deal (it might even help have a smooth transition), this could happen to a limited number of pixels. But you can control/avoid it by tweaking the threshold slider of color reconstruction. You can also use parametric masks to exclude those areas/pixels.
After all, since the tones of these very bright areas will be compressed a lot by filmic/base curve, there is no need to be precise in this stage (before applying those tone mapping modules).
As far as I know, you cannot get real colors by applying negative exposure values because at least one color component is clipped at overexposed regions. Though, even if I’m wrong, you still have the threshold/parametric masks option mentioned above.
This is correct because it works in Lab space. However, here you just want to reconstruct colors (not tones, which are already recovered as much as possible by “reconstruct LCh” mode of highlight reconstruction). Again, you can apply the color reconstruction module in either “color” or “lab color” blending modes to make sure it won’t touch the tone values.