There are two ways you can play MGSV: The Phantom Pain. You can do it through the standar edition or you can get the Definitive Experience. I was wondering if there are differences between the two. I want to do runs of this game, but I only have the Definitive Experience. Is there a problem if I submit runs using that version?

There's no problem with it. We don't ban the use of the definitive experience or DLC items. It might be better for you if you're planning on running new game as the definitive experience gives you 'free' staff members as you progress through the game.

There's a difference if you're planning on running on console though. IIRC you can't downpatch to 1.01 with the definitive experience, only with the standard edition. But with the PC version you can downpatch to 1.01 with both.