Its a little more complicated than that, but it starts with the fact that the CFAV (CNAV? did it recently change from Canadian Forces Auxiliary Vessel to Canadian Navy Auxiliary Vessel?) Jack has no existence in our system of national ship identification. And, no it is not as simple as amending the Manual of Ceremonial, as it is directed by the Canada Shipping Act, which would have to be amended.
In Canada, we have only two possible Ensign: The Naval Ensign, i.e. the RCN's White ensign, or the Merchant ship ensign, which is the National flag. This is different than the UK or Australia, where the identification of vessels allows for three categories: Vessels of her Majesty's Armed Forces (white Ensign), other vessels of her Majesty's government, or vessels in her service, or vessels commanded by members of the Naval Reserves (Merchant ships commanded by a merchant marine officer also holding commission in the NR) fly the Blue, all other merchant ships fly the red ensign.
The reason the RCN can fly its own Ensign is because the ships of the Armed Forces are exempt from the Canada Shipping Act, section 7 (1), which reads:
Exclusion
7 (1) Notwithstanding any other provision of this Act, this Act does not apply in respect of a vessel, facility or aircraft that belongs to the Canadian Forces or a foreign military force or in respect of any other vessel, facility or aircraft that is under the command, control or direction of the Canadian Forces.
A nuance here: this relates to the vessels of the Canadian Forces, not to all vessels of the Department of National Defence. The CFAV's are operated and under the Department of Defence, thus they are subject to the Canada Shipping Act. Therefore, they must fly the Canadian Flag, under Art 64 of the Act, which reads:
Right to fly Canadian flag
64 (1) A Canadian vessel has the right to fly the Canadian flag.
Obligation to fly flag
(2) The master of a Canadian vessel, other than one registered in the small vessel register, shall ensure that it flies the Canadian flag
(a) when signalled to do so by a government vessel or a vessel under the command of the Canadian Forces; or
(b) when entering or leaving, or while moored at or anchored in, a port.
So where does the "Blue" jack of the CFAV's come from? It is used as an identifier of the vessels who operate under tasking made by QHM. That's all it means, and that is why it will not be flown as an Ensign, but only as a jack, or at a yardarm. It is the same reason, for instance, that the Coast Guard has a "jack" but flies the National Flag as ensign.
In the present case, Asterix, a vessel belonging to the merchant service, is obliged to fly the Canadian National flag as her ensign. The CFAV's blue is only flown as secondary indicator that it works as tasked by QHM.