I did that and it turned out beautiful. I was paranoid and kept the spar varnish and stain from the same brand (Varathane) to ensure they mixed well. It also didn't seem to interfere with the straight varnish over the top.
This project was over the winter so I cannot speak to the durability of it, but it looks pretty! I used it for the benches and transom of my boat and then had a bunch left over and used it to seal my braces before I painted them. Didn't seem to bother the paint going over the top as well.