There’s your confusion. Our system of government has what’s known as ‘checks and balances.’ There is no one ‘top guy’ of the government.
There is one ‘top guy’ of the executive branch. His job, at least in theory, is to execute the legislation passed by the legislative branch. But the legislative branch has passed many laws at many different times, and the President is still charged with executing them, regardless of how recent or ancient they are, and regardless of the strictures of this year’s budget that the current Congress has provided him with.
And it’s easy for Congress to saddle the President with a bunch of contradictory requirements, because they don’t have to unravel the contradictions.