A backup is a page by page copy of your database that takes into account the fact that active transactions are occurring so that it has a recovery phase when a restore is run that allows for full ACID compliance of your data at the end of a restore. As Beatrix has already said, the BACPAC is just an export of your data and structures stuck into a zip file. That export of the data is not, in any way, aware of the fact that transactions could be occurring at the time the BACPAC is created. Therefore, when restoring a BACPAC, you could be getting data that is corrupted (deletes half completed, stuff like that) and not ACID compliant. Because of this, it's strongly recommended that you only, ever, take a BACPAC from a database without connections. The best way to deal with this is to create a copy of your database (presumably within Azure) and then create the bacpac from the copy.
They are not the same and are not interchangeable.