Amazing, thank you for the thorough feedback and the great ideas! In particular I think referring to other window managers (especially tiling ones!) for inspiration seems like a pretty obvious good idea in hindsight!
But yes unfortunately the multiple levels issue seems to be a bug! It happens if you touch the end flag more than once (but only on the web export for some reason) - the workaround would be to close the windows and use the level select to continue where you left off.