Physical protection of the primary winding. Possibly better cooling of the secondary.
That commercial unit probably has less primary turns than a microwave transformer (as it was not designed for 100% duty), hence can use less secondary turns.
When you stack to E core sections together you have two primary windings So one is on top one is on bottom. Two primary's will work like one bigger primary with heavier wire. More core saturation for higher power basically.
Being its a short duty cycle there shouldn't be much problem running it this way. Just make sure you have both coils phased right or they will try and drive the E core sections apart instead of pull them together.