Does this:
the Captain of any flight is not the "be all, end all" authority on the initiation of that flight
mean something different than this:
the Captain of any flight is the final authority as to the safe operation of that flight
????
Initiation and continuation/operation are two different concepts. If the plane is able to get in the air safely and legally (albeit with possible operational restriction and consequences which should be communicated by the CA) then if the company wishes to operate that flight is it up to the CA to do so.
I agree with the latter part of your statement though.