With this sort of job the choice of material to do the repair is important and there is a whole raft of materials that are used on flat rooves, etc that can make this job easier and permanently fixed.
Gutter sealant is slightly too thick for this job and doesn't work well on damp surfaces. It's a bitumen mastic designed to 'sandwich' between surfaces, not for sitting on a surface.
A trowelling mastic designed for flat roof repairs would be a better choice, especially if the area is first wiped over with white spirit.
The best choice if access is limited is one of the emergency roof repair sprays. These can work directly on an already damp surface and have a 6 inch extension tube which gives a spray jet effect. The stuff itself 'creeps' well (here, that would be into the seam) and you'd normally put on 2 coats. Depending on the area, you might find that no dismantling is required. Expensive though at around £12 a can.
Finally, just simple flashing http://www.wickes.co.uk/Products/Building-Materials/Roofing/Roof-Flashing/c/1000249" onclick="window.open(this.href);return false; is a great material that can be cut into strips and used for all sorts of things.
Really, apart from the shiny paintwork, the outside of cars are not so very different from the outside of houses and have to withstand the same type of things and so many of the same techniques and materials can be used.
