For reference this was Feast Watson Black Japan. But i don't know if it has anything to do with it. Most of the rest of it is absolutely fine. Just this area which seems to have some large cracks in the binding (which were obviously not visible before staining)
I am just gonna push on - and focus on playability.
So do i just apply clear over the binding? Is that the norm?
That's bad news, CantGuitar. I masked the binding on my ST with pinstriping tape from an autoparts store, and came out alright. But I don't think I was dealing with the cracks as you are. Good luck with the rest of the build.