HERE is a post with a link to Winnebago's roof construction view and sealant instructions. This shows how the roof is screwed on to the sidewall, and how the overlapping thin fiberglass roof is pulled down overlapping the sidewall.
For those that dont know (and I do as I have seen the step by step in person), the fiberglass that is on the rolled edges on our roofs is not glued to the rolled edges of the roof, and it is pulled down over the side walls and held in place by the gutter rail which is screwed into the side walls every 6 inches.
Notice, no where in the Winnebago sealant instructions do they use the word "seam".
I think we are getting confused of what the word "seams" we are talking about. The side caulk does not seal a "seam". It seals the fiberglass rollover to the top of the gutter rail which is screwed on to the side walls. This bead of caulk does NOT seal the roof to the sidewall...it just forces water into the railing and not behind it.
I would only consider where the front cap and rear caps connect to the roof a "seam", and MAYBE is where the OP is questioning about installing the Eternabond. There could be a good place for water intrusion and would might be a good candidate for Eternabond.
I'm not sure what installing Eternabond down the full length of the side gutter rails gives you except that you eliminate re-caulking the gutter...and a person will notice your "fix" from the ground.