Seam between flybridge and cabin - Caulk or Seal?

[kazenza]

I'm repainting the topside on my 81 CT trawler. There is a large seam where the flybridge sits on the cabin. It appears the flybridge just sits on a channel glassed onto the top of the cabin so I am wondering if I need to seal this seam. It is a fairly large gap where the two meet and I just cleaned out a lot of old Caulk from it so I'm inclined to re-caulk it. My questions are:

1) Does this seam really need to be sealed since it appears that there is no where for water to go except back out. In fact it almost appears like water that may get into the wall of the flybridge was meant to be able to get out rather than build up and sit there. In fact along the inner wall the skin is not attached to the channel which I assume is to let water drain out from inside the wall.
2) If I re-seal it what is my best option - 5200? Something else? In some places the seam is nearly 1/4 inch.
3) If I use 5200 to fill it, am I okay painting over it. I am going two tone with the outside of the flybridge and some other accents lauderdale blue. Does the paint hold well over 5200 or should I use some other kind of filler.

Any advise or insight into the construction of these flybridges and the best way to seal this seam or not would be great.

Randy