The lack of a way to change the properties of many layouts at once is a real pain in the ass for big projects.
In some cases, you can override properties with events.
for example, if all the layouts share an events sheet, you can set 'on start of layout' event that overrides certain properties regardless of the layout.
but of course, this won't work if the change you want to make is something like the creation/deletion of a whole new layer.
Alternatively, yes, you can create your own level editor and save the levels via an external file.. but that is a pretty huge topic and i wouldn't actually know which direction to point you in as I have yet to do it myself.