Perhaps it applies only to lone transport assaults.
Correct. It is only lone transports. Any warship, and that includes carriers, can invoke the rule to ignoring the lone sub on defense.
I can’t remember for certain, but I don’t think you can have a undefended trprt in the same SZ as an enemy sub at all. It can move through them though.
Actually a lone sub only prevents unloading of a lone transport. A lone transport may still load troops in a zone occupied only by enemy sub(s) and can move through them too.