I looked at 2 of the cars in the shop yesterday, the rear lip of the gutter is actually part of the sub structure and the filler panel spot welds into the channel, then it would have to be seam sealed.
If you remove the seal, clean the gutter, kill the rust then reseal and paint the gutter the trunk should not leak... the problem with water is the surface tension allows it to wick or migrate into many places you would think that it could not get to.