since I couldn't imagine how Rainbow Dash would actually rape a larger creature

The established character of Rainbow Dash notwithstanding, it's certainly physically possible. For example, it could happen if the larger creature consumed a significant quantity of alcohol or other drugs and was therefore incapacitated. Blackmail or other some other kind of threat could also work. Not wanting to hurt her could also make it harder to fight back. Or it could simply have been Not What It Looks Like.