Well, anything stored by git-annex has read-only file permissions. Apps will follow the symlink, yes, but they will fail to write to the location if they try.

> The way the "check out" feature works is also weird, causing a change in the shared version history.

Unlocking a file changes it from a symlink to a git-annex pointer file from git’s perspective (git-annex accomplishes this via git’s smudge filter interface), but you don’t have to commit the unlock. You can unlock, modify locally, re-lock, and commit the new changed version in one go. It’s nice that you can commit the unlocking action itself if you want a file to be unlocked in all clones of the repository. You can choose whether to commit the unlock depending on if it fits your use case.

For curious readers, https://git-annex.branchable.com/tips/unlocked_files/ discusses these topics in more detail.