They are not "different companies".
Air Nova, Air Ontario, Air BC, Alliance, Cdn Regional, WERE all Subsidiaries of Air Canada at one time or another.
Here are the current Subsidiaries:
Aeroplan
Air Canada Cargo
Air Canada Ground Handling Services
Air Canada Jazz
Air Canada Jetz
Air Canada Technical Services
Air Canada Vacations
Employees of these companies ALL have status and/or benefits at Air Canada.
The "rights to seniority" you speak of were negotiated as part of the various collective agreements.
Jazz pilots get some nice benefits when they "transfer" to Air Canada.
Inter Canadian was a different story:
At one time their pilots were offered a merge with Canadian Regional but they chose to retain a separate seniority list. The F/A's did decide to have a merged list. When Inter Canadian went under, some F/A's used their seniority to transfer to different bases. The pilots were offered employment at the bottom of the list and some did get hired.