Although I do agree with you from a DBA perspective it was a decision by the team a few years ago and we still follow that decision.
I do agree with you that searching is not as easy or updating multiple entries is not as easy as it would be with a simple SQL DML script.
But keep in mind that our users are not DBA's and often have zero knowledge about technologies required for and used in their server.
Our users rarely have to do mass edits, but they overwrite certain fields quite regularly, which is easier in a YML/text file for users with no database knowledge.
Having said all that I still have to come back to your errors and tell you that those are all errors on your end.
Each of our commits is scanned with different CI tools and checking if the database contains any kind of errors is part of this process.