Yes, that mysterious cloaked figure in Fantastic Four is indeed played by Robert Downey Jr. – as confirmed by the director himself.

The Fantastic Four: First Steps opts not to show how its heroes obtained their powers and became forces for the greater good.

Vanessa Kirby addressed questions about Robert Downey Jr. appearing in Marvel’s 'Fantastic Four: First Steps' post-credits scene

After a number of false starts, the Fantastic Four have another feature adaptation in the retro-pastiche Fantastic Four: First Steps.

Vanessa Kirby addressed Downey Jr. as the “Godfather” and revealed to Variety that it was indeed him in the Doctor Doom suit in the post-credits scene.