I have received a message from Google Cloud Support about this. Discounted instance hours are currently not applied before the daily quote is used to disable the app.
So, even if you commit to discounted instance hours, you have to set daily quote as if all hours are charged at full price, or your app will be disabled.
Google Cloud support writes:
our 'Daily budget' system doesn't take into account discounted instances hour rates in case you ran out of instance hours. It would attempt to plan for the worst case scenario of being charged at full price instance hours.
and, later:
It is, indeed a problem on our end ... we currently don't have a public tracking system in place for outstanding issues nor can I confirm an ETA on the resolution.
We are currently working on making changes in the billing system and your input will definitely have it's weight in the scale. Any new release or updates would be announced at our Google Platform official blog at http://googlecloudplatform.blogspot.com.