Do you know if Jujutsu addresses these issues?

jj does not have large file or submodule support, but it does intend to in the future (you can read their design docs). Right now it's git compatible, so I'm not sure how 'permissions' would be stored compatibly, or what that means. I'm guessing ownership and xattrs

With the git backend, jj inherits git's problems. So right now, it does not, at least directly.

With other backends, it inherits their problems. But also their solutions :) So with those backends, it could!