I didn't install a skylight, but I did replace a ~8" bathroom vent with a 10" Solatube. I figured it would make more sense to have that install coordinated with the Solar Roof (mine is a v2) install rather than to install on the old roof then immediately change things, but in the end that was a nightmare. Getting Tesla to coordinate with the Solatube installer was like herding cats, and when I finally got them to recommend a date for the Solatube installers to come out, Tesla decided to stay away that day, leaving the Solatube installers completely on their own and unable to do anything on the roof so they could only do half the install and left Tesla fumbling with the rest later. I also wasn't thrilled with how they handled the extra vent that had to be added to replace the old vent, even after talking to them many times about it, sending them specs of both of the roof penetrations, etc.
Personally, I'd suggest doing the skylight first on the old roof, based on my experience. It might still be a challenge to get them to recognize the change and update the drawings to match if they've already done them, good luck with that.