I assume the roof repair will be eventually covered by a shiny new solar panel. So, the repair does not have to be " like new ". Perhaps, just unobtrusive, water tight and rust free.
In that case, I would suggest, perhaps a circular aluminium plate. The 2 surfaces must be painted ( the roof and the aluminium plate ) at least on the 2 sides where they mate. Do not use any fixings, apart from an appropriately rated Sikaflex type of adhesive/ sealant. The two mating surfaces must be kept apart by means of the adheasive. This is to prevent any future galvanic corrosion. Thus, no other metallic fixings are to be employed.
As for the headliner repair ... don't try to hide it. Make a feature out of it. Example, install a led light. Perhaps puck style. A battery one will do, if running cables is not feasible.