Checks-and-balance relationship between the executive and the legislature collapses because the legislators partake a responsibility of the executive. As such, they become subsumed under the President being the head of the executive branch in the execution of the budget--a violation of the separation of powers.
That checks-and-balance relationship exist for a reason: it is precisely to prevent actions of the executive that could already be beyond and abusive of its powers. Because this could happen intentionally or unintentionally.
It is possible that because of the intention to serve (to provide resources for priority programs and meet the needs of the people), the executive overlooked (intentionally or unintentionally) a legal provision.
Here are five areas to watch in the new set-up to make the reformed pork less fatty