Setting SQLAlchemy autoincrement start value

You can achieve this by using DDLEvents. This will allow you to run additional SQL statements just after the CREATE TABLE ran. Look at the examples in the link, but I am guessing your code will look similar to below:

from sqlalchemy import event
from sqlalchemy import DDL
event.listen(
    Article.__table__,
    "after_create",
    DDL("ALTER TABLE %(table)s AUTO_INCREMENT = 1001;")
)