I'm struggling to understand what the issue that the author is getting at. The point of a database is that it's ACID compliant, wrap insets/updates/deletes in a transaction and no such drift would occur. What am I missing?
Much more likely I think is that you can’t use the db to prevent invalid states here (unique constraint, etc) and you’re dependent on other areas of the code correctly implementing concurrency controls. Race condition in resource A causes problems in your permissions table now.
And just from a general engineering perspective, you should assume things are going to fail and assess what your path forward looks like when they do. Recovery script sounds like a good idea for a critical area.