They claim that they deduplicate runtimes. I question how much can really be shared between different branches when everything is recompiled. How much has /usr changed between releases of Ubuntu? I would guess just about all of it.

Storing applications in a local OSTree repository has other advantages. For example, it allows files that are stored on disk to be deduplicated, so the same file that belongs to multiple applications (or runtimes) is only stored once.