As the GluBoost is basically clear CA, in theory you should be able to ignore the ripples and just keep on adding your clear coats. You may need a few more coats of clear than originally planned because of the ripples, as when you sand back flat you’d really want a surface that’s all clear coat, with no small flattened ridge of GluBoost that’s poking through. Whilst the GluBoost is transparent and should polish up just like a clear coat, it’s reflective index is probably slightly different to the clear coat so it may show up as a very slightly duller or brighter patch (though it may not).

So I’d just add more clear until you’ve got enough depth to endure that you don’t sand through to the GB ridges and leave those covered with clear.

The GB filler was probably not the product to use on a stained surface just as a filler as you should really should sand the surface flat after applying, which means you are likely to sand off some stain when doing so. I’d assume it’s meant more for use on bare wood. If you applied enough GB to sand it flat without breaking through to the stain, then you’ve got enough protection to just polish the GluBoost to a shine and not bother with a clear coat. Though if you are applying decals to the headstock you’d want clear over those for protection.

If you sand off some stain, then that means the wood should be exposed and free of GluBoost in those spots so it should take up more stain, but it may look a bit patchy around the edges of that area where there’s a mixture of exposed and partially GB covered wood. It may depend on how saturated the wood was with stain to begin with. If the wood was stained until it didn’t get any darker, then in theory, you should be able to stain and stain again and achieve the same colour. But theory and practice don’t always match, so I’d take the less risky route of just applying clear.