You don't need to go up to root; you can hold Q W E to open up the dial at various levels of the tree depending on your current tile. Typically (i.e. following the design of the official dungeon) you'll want to use enemies from the same biome - if not, you're free to freestyle it but yes it'd take longer to switch. I don't see how a menu would really solve this though; perhaps you could just have a long tree list but it'd still take some scrolling to get to another biome.
In regards to the dungeon editor, apologies, I meant info on the bug. Yes, you cannot play dungeons outside the dungeon editor, but playing a dungeon there is the same as playing it from the menu really. Just, only with the first character. It seems as though you can load them now so I guess all is well then.
The reason why it saves a copy of the levels inside the dungeon and why you have to update them manually is so that you can freely share just a dungeon file with someone else and they can then play it right away. If you also had to share all the level files it'd become a very bothersome process. In the future, this will be simplified by having a button to update the levels and update all, and probably an icon to show there's changes.
Unfortunate side effect there with the meadow tiles. I'll work up something to maybe delete them once they're offscreen, thanks!