Re: Arauco plywood good or bad
Edit: Short answer - nothing different from installing any other plywood. It's not super rot susceptible or anything, it won't rot faster than 95% of the other plywood you might get, including marine plywood.
You don't need to soak it in resin. For poly, what you want to do is coat it with a thin layer of resin and glass... maybe 6 oz. woven or .75 oz mat if you're just waterproofing. If you're using biax with mat that works too, but using that for waterproofing is overkill. Just glassing it so that all wood is covered would be good, including the part where it gets glued to the existing fiberglass skin.
For attaching to the existing skin, I'd use either poly glue or thickened resin for lamination... resin mixed with chopped fibers and cabosil, or wood flour. Basically you make a thick resin that won't dribble out the bottom of the joint. Clamp together using through holes or biiiig clamps.
Or if you're talking about mating the edges of the transom with the hull sides and bottom, that's different. For that, fill any gaps along the sides and bottom with glue as above, then use two layers of 17 oz. 4 inch tape, offset by at least an inch side to side (for wider coverage) along the seam, making sure you get all the bubbles out. Once that's done you can cover the whole transom with thinner glass if you like to protect it, or not if you've already done that to waterproof it.
I'm assuming you've done this the standard way, by removing the inner skin of the transom and then the rotten wood.
Finally, for waterproofing penetrations the 5200 is good, but here's what's best: Overdrill each hole by about a quarter inch using a bigger drill bit, then plug the entire hole with a mix of resin, cabosil, and fine chopped fibers. If you're concerned about appearance then fill the outside skin with gelcoat and smooth it, or else drill a pilot hole from the outside then counter-drill from the inside to get the oversize hole without penetrating the outside fiberglass skin. Then fill the hole from the inside.
Once it's hardened, re-drill the hole the appropriate size for your attachment/bolt. That way even if the 5200 or whatever leaks, all water will get to is the hardened resin and not the wood.
Erik