Only putty tape under my Corner Cap Rail?

Hi, yes, planning on replacing rotted wood - corners and a few rafters. This type of camper doesn't have the foldover of the roof skin to the side skins. They literally just butt up against each other and are covered with the corner cap (difference than J rail which just attaches to the side of the trailer). I am not replacing the metal. Do you mean using aluminum tape under the cap rail?

Scotty has the same kind of cap rail. There was an obvious gap between sides and back on all 4 lower corners which was caused by wood rotting and swelling, then getting abused by PO, etc. Once I replaced ALL the wood, that problem was solved. I seriously doubt your trailer had that skin gap when it left the factory as they cut the side skin flush with walls and then installed and cut the roof skins flush to the sides. Once you replace that rot, you should be back a better edge joint.
Here is a product we heard about back in early Spring that got some positive reviews and might be an answer, but it needs a clean (like new kinda clean) to stick well. It is said to be flexible enough to forgive slight movement as you trailer rolls down the road. They have a vid on applying it...

catalog.sealdesignllc.com/product-category/seal-tite-corner-seal/

I think you do need something on the butt joints. I would use waterproofing tape and trim it if you need to so it doesn't show under the cap. It's going to be dicey because of the skinny overlap on the side.

Also, I would use pure butyl tape on the caps. It is stickier and seals better/longer than RV butyl putty.

OSI gutter seal is great stuff and can be used as a primary sealant before the above. You're going to have to let the trailer tell you what it needs.

Get the wood fixed and post some pix. We will help.

GS 121 is the same thing but is a waste of money. It dries out in the caulk tube. If you get the smaller toothpaste type of tube, it will last years. Also much easier to use and control...

The first thing to do is rebuild the trailer and reframe so the metal fits as tight as possible. The metal will need to be nailed or stapled in place. When everything is as close as you can get it, sparingly dab OSI on every divot or hole, as well as the staples/nail heads. LESS IS MORE. Smooth with a paint thinner dipped finger and let dry.

Now you are ready to assess the joint and decide what you want to do. Waterproofing tape will protect the joint but it does add some thickness. I don't often use the tape. You might do some heavy research on something sticky but thinner that might span the joint. It must be discrete.

Finally, you are ready to add the cap rail. Use butyl on the cap, both sides. You'll pry have to trim to fit. if you clean the scissors frequently, it will help. (paint thinner)

Many times, if you have removed skin and then tried to put it back on and the roof doesn't fit again, it's because the trailer is out of level and plumb. Try jacking up one corner at a time either front or rear and see what happens. Usually, once you find the corner that needs to be lifted a bit you will see the metal begin to line up.