I don't know the "correct" answer for you, but here is what I'm thinking.
Each site has it's own index.php file that points to a shared app and then if you need to take one or two down you can just replace index.php with something else. Then replace it back when you want them back up.
The issue I see with have multiple "app" folders is you are going to run into a nightmare keeping them all in sync.
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