I've used Minwax Polyurethane Spar Varnish.
Haven't used the varnish you are planning.

There is only one issue I have with the method, and I haven't found a solution yet.
The varnish will randomly penetrate the polyester deeper at some points over the frame.
This causes that area to be darker at that point, leading to a blotchy look.
Once the varnish has dried, you can reach in and stretch the skin, breaking the bond between skin and frame, which removes the dark blotch. Except you can't always get all of the dark spots broken free.
More to the point, you can't reach into the ends of the boat to remove the blotches there.

I've tried pigments, in the form of Minwax stains to color the varnish. This spar varnish does not come in colors, and I have not tried other pigments.
You really need to make a test piece and try out your stain/ varnish combination - the colors are not always easy to predict.
The last one came out much more yellow than was desired. And the light percentage of pigment did not hide the blotching. Previously we did a higher percentage of a different color which came out more like paint.
I'd encourage you to try plain varnish, personally I like the color best (except for the blotching).

When I asked about cures for this issue (on this forum) it was suggested that I wax the frame. This may have reduced the blotching, and probably made it easier to break loose the blotchy spots. I still ended up with dark spots and finally painted the skin (white).
It was suggested that I first do a lite coat of varnish to seal the skin. Unfortunately the second coat penetrated and made the blotches.
I was also told that use of the kayak would flex the boat and break loose the penetrated varnish. Didn't work for me.

One suggestion: Do not thin the varnish for the first coats. I did by accident (I already had some thinned that I used) and the blotching was more extensive.

I'm getting ready to do a trial on a test piece where I'm going to paint the contact surface of the frame white. On a previous test piece, it might have eliminated the blotching by having a light surface where the varnish went thru the skin (normally I'm using varnished cedar for the frame, which is quite dark).

Dave Gentry, at Gentrycustomboats.com actually waterproofs the skin using Loctite PL Premium put on with a squeege. If you can get very thin it has little color. You do need to practice this application, for me it is difficult to apply evenly.
I do use this over the bottom stringers for better abrasion resistance.
Gentry says you need to coat it with something to provide providing UV protection. Spar Varnish would do.

Well, that is enough of my failures.