HTML elements don't actually belong to a layer. For example you can't overlap them with a sprite on a layer above them. They essentially float on top of the canvas. Things like buttons also have their own ways of blocking input, in this case via the "disabled" attribute. Should making a layer non-interactive make HTML buttons disabled even though they don't actually display on that layer? I'm not sure it makes sense.
I think Construct probably needs a special "HTML elements" layer that appears on top of everything else in the editor, and all HTML objects go on that layer. It would clear up confusion about things like layering that regularly come up too.