Hi,
The All Reports pages work by asking for all reports sent to a particular body. In theory you could add a hook to the point at which it queries this, and then add the national road agency body there, so that its reports would be returned as well, but then that would be their reports anywhere, not limited to the council's area. You might be able to filter on `areas` I guess to work with that, but I wouldn't be exactly sure how.
On your second query, there is a categories_restriction hook called with the list of categories that have been fetched by that point. You could in theory do a check there and change the road agency category to be staff only at that point, though I'm not sure if that would be the only place it would need doing, but would certainly get you a lot of the way.
ATB,
Matthew