This just sounds like when the script is run, a lock is taken. It seems like a pretty fast and loose definition of "atomic" (as in, not the ACID sense), as it says below:

     If a fatal error is returned, the channel program may have not executed at all, may have partially executed, or may have fully executed but failed to pass a return value back to userland. 

If an external tool is allowed to acquire this kind of exclusive lock, I don't see the difference.

> If an external tool is allowed to acquire this kind of exclusive lock, I don't see the difference.

That's the whole point, as I understand it. The channel programs are executed in the kernel, in a way that cannot be done by external programs. Some more details here[1].

edit: I also think you should have included the note, which says

Note: ZFS API functions do not generate Fatal Errors when correctly invoked, they return an error code and the channel program continues executing.

So while it's not quite ACID-level, its not as bad as it sounds without that note.

[1]: https://openzfs.org/wiki/Projects/ZFS_Channel_Programs