I believe I can be of some assistance, I have an early hardtop (with ears) and the Porsche Roof Transport System (RTS). Firstly, the only difference between the two hardtops are the ears, which is just a small plastic cap behind the windows which you can pop off to mount the RTS. However, Porsche quickly abandoned this design and removed the ears from the hardtop.
The RTS was sold with mounts to be fitted to hardtops with ears or directly to the body by popping off the 'wingtips' just behind the door / in front of the clamshell. When the hardtops with ears were discontinued Porsche issued a TSB which advised everyone to mount the RTS directly to the body (under the wingtips). I have mounted my RTS both ways, and suggest the body mount (under the wingtips) because it is a lot sturdier and quieter.
To your other question, the RTS is the only rack available for the 986, unless you are looking for a trunk mounted luggage rack. I am actually surprised Porsche even made a roof rack for a convertible, and no one else offers anything 986 specific or universal that would work. The main problem is that the roof has too much of a curve to stick or clip anything to it.
I even investigated mounting a ski rack to a trunk mounted luggage rack, but that presents two issues. The trunk racks cause paint damage and the angle is not steep enough to clear the top. I suppose you could weld a rack onto the hardtop, but it's made of aluminum and there is a good chance it would deform under any significant weight. The RTS is rated for 175 lbs.
I have a 6' Thule box I mount on my RTS in the winter, and a few others have mounted bike, surf, kayak racks. The RTS bars are oval and you can use most generic ski, bike, etc carriers. I will say my 986 handles horribly with a roof box, way too top heavy, and I bought the slimmest box available. But it sure looks cool.
Hope that helps!
