Hopefully I have cleared that up.
Facebook, who operate one of the largest relational database fleets in the world, have used declarative schema management company-wide for nearly a decade. If engineered well, you end up with a system that allows developers to change schemas easily without needing any DBA intervention.
I viewed the author as targeting smaller dev shops who don't have a dedicated DBA/expert. Groups who might use an ORM's migration framework for example. In which case, it would appear that there is significant loss in migration flexibility if you remove application code from the architecture.
For example, say you need to populate a new column based on data in other columns, across an entire table. If the table is a billion rows, you can't safely run this as a single DML query. It will take too long to run and be disruptive to applications, given the locking impact; it will cause excessive journaling due to the huge transaction; there can be MVCC old-row-version-history pileups as well.
Typically companies build custom systems that handle this by splitting up DML into many smaller queries. It's then no longer atomic, which means such a system needs knowledge about application-level consistency assumptions.