And RF never stated he beat Kara's cousin. The exact quote goes like this, "Yeah, your cousin is fast. I'm faster."
While it can be implied RF beat Superman, this isn't solid proof that he did. For all we know, Superman was on the verge of beating RF but Thawne used his superior speed to get away. Superman gives chase but can't catch him because RF is faster.
But we don't know if that happened either because we don't know what exactly happened in their encounter. One thing about implied statements, though, is I don't take them as fact. Plus, RF could have been lying just to intimidate Kara.
Maybe they fought in that Crisis event to happen 2024?