In my recent dealings with MySQL, I learned that some connection string options affect the behavior to such an extent that the code will break unless they are set correctly. To prevent the application failing because somebody configured the connection string wrong, you can make sure in code that the selected options are set correctly.
Using Entity Framework Core for loading large amounts of data into database is not very efficient. The bulk operations from the EFCore.BulkExtensions NuGet package can help in such scenarios. Unfortunately, not all of them work (yet) for all database types.
I've been recently involved in migrating a .NET project from Microsoft SQL Server to MySQL. While most of it went pretty smoothly, we did encounter some challenges with GUID/UUID values.