I haven't done a guitar yet, but I've done a TON of samples over the past 8 weeks while waiting for my kits to arrive. I've tried several products and combinations, and learned pretty much what Simon just said

You can use a spray-based sealer between stain and top coat. I've been using Watco Lacquer Spray (which is nitro based) and it's really an awesome product - sprays incredibly easy and wide, little to no touch-ups required, dries fast, and works with most top coats (you need to check compatibility with whatever top coat you're using.)

1) Brushing or wiping water based sealer over water based stain is bad - too much stain interaction/movement.
2) Lightly wiping oil based sealer (or true oil) over water based stain is possible, but the applicator still picks up color so need to change frequently.
3) Applying 2-3 light coats of spray can sealer seals the stain enough that I can hand apply a top coat in thin coats without much trouble. If the top coat goes on too wet it still will pull up stain.

All of the basic lacquer/poly sealers are some proportion of solids to carriers (liquid). Ballpark 10-20% solid, 80-90% liquid. They're wet when you apply, and the carrier evaporates leaving behind the solids. So realize that whatever product you put down is going down as 80-90% liquid which is what causes interaction with the stain. This is to illustrate the importance of using light coats.

True Oil is probably a little different. My guess there is that oil doesn't mix with water as easily as solvents or water-based top coats, so you can get away with it if you use very light coats at first. I was successfully able to wipe on layers of True Oil over water based stain, but the small sample took a lot of care and attention to prevent stain interaction so it's not what I'll use on anything I've stained with water based.