I use EF core and instrument all my queries - if I see a slow one I hand optimize it. Best of both worlds I think - and I say that as someone who loves to fiddle with SQL.
Also worst of both worlds - you need to know very well both the underlying database (SQL) and also the complex leaky abstraction (EF Core) and how are those abstraction translated into the SQL.
I'm no ORM hater (use Hibernate daily) but claiming that using ORM will simplify working with the database is at least misleading.
For some reason people think it's okay to be ignorant while using an ORM. What you are interacting with is still a database! Treat it like one and you will save a lot of time in the easy situations.
Pretty sure SQLA the ORM has nothing to do with schema migration, which is usually handled with alembic, the sister project. Not sure about Sequelize.
Now, there’s nothing magical about alembic’s handling of renaming or deleting columns for SQLite; it has to recreate the table just like what you would do if you’re hand rolling the SQL, so it has the same problems.
But if you're using SQLite for simplicity there's a good chance you're not interested writing raw SQL statements either.