CRA is almost a separate entity from other federal departments, so it behaves like a private business than a government department. They aren’t even at the behest of the treasury board.
The CRA is its own department, like any other department. It is structured and operates just like any other government department as opposed to a private business.
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.
I recommend you look up the purpose of Treasury Board. They are the corporate treasurer of GoC. All expenditure requests go through them and if insufficiently justified then Treasury rejects them. And the requesting department/division/establishment must resubmit. It even applies to CF/DND too.
(In some countries/companies this function is called the comptroller or the controller.)
I think you have a some what confused understanding of what the various roles and duties of these government bodies are. Whatever the purpose of the Treasury Board is (which you do not seem to fully understand since they are not a corporate treasurer), it has nothing to do with whether the CRA operates as a corporation. Furthermore, the CRA is not subservient to any other federal department as it is its own department chaired by the Minister of National Revenue.
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:
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.
For one reason or another, collective agreements are signed directly between the CRA and employee unions. Collective agreements for other departments are signed with the Treasury Board. No other federal department with civilian jurisdiction holds this kind of exceptionalism.
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.