When I built my first kayak I coated it with epoxy and started paddling. After 18 months the epoxy had turned quite cloudy. I am now in the process of sanding much of the cloudy epoxy off. (Which means sanding down to bare wood in some places.)

On my second kayak I also needed to paddle it before varnishing. I took some short trips on cloudy days and transported it deck side down. (I'm going to paint the hull). I've got the deck varnished now and it looks much better than any epoxy finish. I'll probably use it one more weekend before I paint the hull and get full UV protection.

Epoxy can get pretty cloudy pretty fast. I could see the shadow of the tie down straps after the boat had been on the car all day.

By all means protect any parts of the boat that you ultimately want to varnish, even if it's a couple of quick and dirty coats that you'll sand off later. It easier to sand off the varnish that cloudy epoxy.