Entity 01 knows about Mario Entity's presence, yet didn't create him. The information on him is so little. Plus, how would Entity 01 be able to create the Mario Entity if he himself cannot alter time? The Mario Entity managed to rewind time back in FNaW 2. Yet Entity 01 only has enough power to send a ritual book back in time, and not send HIMSELF back in time.

At one point, Entity 01/Emma decides to make Virus Mario based off of the only information they have of the Mario Entity. Likely praising Entity 00, as he is likely the one who made the Mario entity.

The Mario Entity on another behalf may very well be one of Entity 00's creations that tried to escape the Overworld when he was brought to Real world when the Morning Star Company discovered him. The only freedom he got was the pocket dimension the Morning Star company managed to trap him into.