This is a run-around on Congress.
He cannot do a line-item veto (the SCOTUS found that illegal).
But he does have the authority to not spend any funds he doesn’t deem necessary, and he returns them to the US Treasury.
So Planned Parenthood? He can just simply not allocate the funds per HR 1625.
The Omnibus spending bill is not a budget, which would require the president to spend the money as prescribed in said budget. Rather, this bill only puts forth guidelines on how to spend it. This is the same thing congress did with 0bama for 8 years. And for 8 years, 0bama signed the bill then threw away the “guidelines” and spent the money how he saw fit. By invoking these clauses, Trump has done the same thing.
He knows how to play their game.