Once the rust penetrates the channel, water enters the trunk and will eventually rust away the trunk floor. The only fix for this problem is to replace the rusted metal with new metal and fill the channel with clear silicone to prevent the water from sitting in the channel. A better sealer for the channel if the surface is not prepared properly is black urethane. New cars are using this sealer and it is extremely durable and can be used to replace the butyl window ribbon to seal the glass to the channel. Black urethane is available at NAPA stores as well as auto glass shops.
Convertibles have several problem areas.
The first one is the top mechanism. If people have sat on the top when it is down they will bend it out of alignment preventing proper operation when raised. The tops also have a tendency to split above the side rear windows due to the padding moving while the top is being lowered and the mechanism pinching the top material. To prevent top pinching, make sure the pads are directly over the mechanism as it is being lowered. They have a tendency to move inward as the top is being lowered.