Under the system of responsible government, the government has an obligation to make the case for Parliament that what they're planning to do with taxpayers' money makes sense. On the basis of those answers, Parliament either approves or rejects proposals for funding. That's why government comes to Parliament to ask for the money.
On your notion of accountability, the picture you're painting is that somehow Parliament is meant to hold government to account without any leverage, and that it's immaterial to parliamentary accountability how it is that government intends to implement a high-level goal.
If the high-level goal is supporting the Canada Border Services Agency, there are a number of ways you could do that, and it makes perfect sense that Parliament might approve some ways and not approve other ways. The point about vote 40 is that we're now being asked to approve that funding without knowing the way in which the government intends to pursue that high-level goal.
Do you not agree there's a problem in the basic notion of accountability that represents?