I totally understand what you mean.
In both scenarios you listed, (Making a change to a layer means going to every layout and making the same layer change, and level editor layer stuff) I have had to deal with as well.
It's like a matter of pre-planning what layers you would want and what settings/effects you want, make it in one layout, then duplicate that layout. But you best hope you don't want to tweak a single setting in a layer, because then you'll need to fly across every single layout to manually make the change (or possibly edit the project's files to apply the change quicker which is risky and a bad idea in general to tinker with things like that).
The ability to add layers at runtime sounds like a dream, we could then have 100 layouts, decide "Hmm, I want a HUD layer" (if you somehow didn't think to add a HUD to your game after making 100 layouts lol), make an event "Create layer : HUD" (probably have an index for where to z-order the layer), and then all other events already exist to tweak the settings of layers (minus a few, like adding new effects). Would be awesome.
tl;dr: I agree! +1