Gel stain, or any stain for that matter, is not a "Finish" (despite what the can says.) They have a small amount of binder -- oil, varnish, lacquer, or whatever. When used between coats of finish they are functioning as a glaze and must be top coated. How well the top coat sticks is a function of what finish is on now, what you are applying, how long you let the glaze dry and how thickly you applied the stain (remember it has few binders so thick coats can be problematic.)

I view gel stain like shoe polish, it does not penetrate that much, and sits on the surface. When I apply it I just buff it on with a cotton cloth. Then topcoat with a compatible clear coat.