I've been a little gun-shy of water-based stains after seeing several boats where the final color changed radically from the intended color after the application of epoxy. One was supposed to be a black that turned deep green, the other was supposed to be a cordovan mahogany (deep red almost hinting at purple) that came out brown hinting at green.
The brown from the cordovan mahogany was a pleasant color even if it was not the intended hue, but the greenish black caused the builder to paint the boat.
Since epoxy and varnish often have some color (usually yellow/amber) it is expected that the tone of the stained wood will change a bit as you build up coats over top of it. But the color changes on some of the water-based stains I've seen were something beyond this. Something about the chemistry of the stain and the epoxy interaction completely changed the color. It is like someone has spun the color wheel.
I know people have had very good experience with some water-based stains, but personally, I would not proceed with a color until I had tested it thoroughly.
I have literally tested every color of Behlen's Solar-Lux stains and have never been surprised by the color change. They always result in the expected color. A blue stain with yellow/amber varnish will appear greenish as one would expect. It only nudges the color wheel in the direction of the coatings over the stain.