Let me get this straight Dickie: The Targa-top openings were filled (somehow) and then Boat Fairing - which is an Epoxy - was used to fill in the area and make it smoother, yes?
Epoxy is more or less the same weight as polyester filler.
And yet, you don't want to use a skim of polyester filler?
Am I missing something?
Buy yourself a few wooden rulers of varying lengths (300mm, 400mm & 600mm) and wrap your 80-grit sanding paper around them.
It'll follow the curve of the roof without creating divets.
I have a professional 'Splining Kit' for this job, but the rulers will produce a similar outcome.