Basically, you need to match the structure from the thing you're overriding
hmm, i know in previous version of SS that wasn't necessary
is there something I can add to my theme.yml to modify that?
or is that just the way it is now in SS4?
No.. that's the way it works now. It's actually a better way to do it, as it takes away the possibility of conflicts between modules
Is it possible to use logic in a page controller to choose between 2 different Layout templates?
if $currentMember is in group A then use layout template A else use layout template B
Yes. You can do it in a couple of ways.