The best approach I found by using init_queires()
Since you are transferring WordPress data to Q2A tables you can create missing tables using init_queries() and do all transfers on the fly while creating tables. Like transferring user, user role and permission, etc.
Init_queries() also can delete WordPress tables and so once data transfer you can delete those. After that you just need to remove the WordPress path from qa-config.php file.
Only one thing I am still looking for is to transfer a password since both systems has a different approach to create a password, user must have to reset it once Q2A has been separated.