in theory if you follow a good naming convention, only layers that need to be synced would share a name, and so you could say "for every layout that has a layer named X and a layer named Y, move layer X to a given position relative to layer Y"
Same would go for renaming, removing, adding or editing.
This would be kind of a pain to set up the first time for existing projects where the naming convention wasnt made with this feature in mind, but for everything else in the future you could in theory do it that way.
I also agree that layer templates sound like the best way to design the feature in an ideal world, but I would rather have a simple batch edit feature than an over engineered half broken new layer system that takes 4 years to get right.