Also, now that I took a minute to think over your proposal, I don't see how this works for my use case.
The value in hyperkey is that it is usable in any app, not just BTT. For instance, I want to map global hotkeys so that hyper+v opens my clipboard history app and hyper+j opens my calendar and hyper+t opens my timer, and so forth. These are all mac apps that support global keyboard shortcuts that I want to set in such a way that I ensure they don't conflict with any other built-in keyboard shortcut for any other app that might be in focus at the time.
Maybe I'm misunderstanding your suggestion but it seems to be a nonstarter for me.