They only dedup runtimes, not individual dependencies.

No, not quite. Flatpak is containers - it just stuffs every dependency that an application needs in a directory with no way to deduplicate or update independently. Gobo is a bit more nuanced, since dependencies are shared between applications when the versions match.

I think the main premise is that every version of every software has its own installation prefix. This allows you to mix&match different versions, perform atomic upgrades, etc. You can think of it as a proto-Nix. TBH I don’t see much point in it now that Nix(OS) and Guix exist, or, if you don’t like their purity, stal/IX.