As I understand it, an omnibus bill is not a budget; it grants the President discretion to spend the money, or not. The bill only provides suggestions on how to spend the money.
The President is not bound by the bill. It is the same method that was used to fund the government for all eight years under the previous president. It grants tremendous power to the executive branch by default. It may be that the “wall” just got funded under the DOD.
I am not an expert, but that is how it looks to me.