They are not at the behest of the Treasury Board because the Treasury Board is a committee, not an administration or agency. The board has no executive authority whatsoever and exists to give advice to Cabinet rather than to perform or execute a duty. However, the individual members of the Treasury Board do have the ability to order the CRA, principally the Minister of National Revenue, who sits on the Treasury Board, is the executive of the CRA.
Perhaps you're thinking of the Bank of Canada, which is an actual corporation and operates in a semi-independent manner from Parliament, although technically Parliament has full oversight and authority over it.
(In some countries/companies this function is called the comptroller or the controller.)
Canada does have government bodies that are corporations, as I said the Bank of Canada is one of them, Canada Post is another. The full list can be found here:
https://www.canada.ca/en/treasury-board-secretariat/services...
The CRA is no where on that list.
Here's a bit of a challenge for you to help you clarify your understanding of this. Find one single semi-authoritative source that refers to the CRA as a corporation or describes the operation of the CRA as being like that of a corporation. I'll even take an informal source.
You won't find any, since no one describes the CRA as a corporation and doing so is just confusing. You made it up, and given that Canada does have bodies that operate as corporations, you shouldn't be surprised that making something up like this will elicit disagreement.
Even the Canadian Coast Guard collective agreement is signed with the TBS.
I think these minor variations in corporate structure (or whatever you want to call it) embolden certain departments to go their own way, and forget their place in the whole of society.
See also the Canadian Mint copyrighting the penny.
(1) http://www.ipbrief.net/2012/09/20/a-cents-of-pride-royal-can...