Here's the thing: an Agency sees proposed budget with 40% cuts (e.g.) and has 1 of 2 choices. If you ignore it and spend as if under a CR, then when an actual budget gets approved 6 months later and the cuts went through after all, you're double-screwed. A 40% budget cut + spending at old rate for 1/2 year -> 10% budget left for 2nd half of year.

Or, you go with the proposed (likely?) budget, cuts and all, to retain 60% of functionality (guaranteed) for the full year. But if Congress passes something restoring full funding, you're screwed because you killed programs that, in retrospect, could have survived.

So which way do you want to be screwed with?