I found these rules here
The mast destroying mechanic is definitely just there for balance. Otherwise A) what would you do with large ships without crew? and B) this would obviously be overpowered af. Perhaps you could find a middle ground where the captured ship must sail back to your home island before it can be given anything other than a move action or something like that.
One boarding roll per turn would mean that you can’t conduct this action all at once. You eliminate one crew/mast a turn. So in the example above it would take the Zephyr four turns to finish the boarding action and capture El Leon. Over the course of those 4 moves, El Leon can’t move or shoot, and Zephyr can’t shoot and can’t move unless it becomes no longer pinned.