What could they have done differently?
The team recognizes they should have prioritized only one refactor. For example, they could do #1 during a single Sprint, and immediately release a new version with updated Symfony, ORM, Job Scheduler and many other niceties.
Then, map Doctrine entities to their existing tables, without creating a second database. From then on, new tables would comply with industry standards. And, in the background, they could refactor the old data model, and perform single migrations. With no hourly “Sync Jobs” moving data between 2 databases.
This approach would not have made all the refactoring work go away. But it would have given the team all the power of an updated, full Symfony framework, while allowing them to do the data refactor in the background from day 1.