I think the head to head with Nadal would have even worse impact on Federer if Nadal were a future greatest ever contender which he isnt.
An example I can think of is the Navratilova and Evert rivalry. Evert nearly everyone has in the top 3 or 4 of all time. Yet nearly nobody considers her a possible choice for the greatest ever. Graf, Navratilova, Court, and even ones who the vast majority rank much lower all time like Connolly, Seles, and Serena have more "the greatest ever" backers than Evert. The reason for that seems pretty obvious to me. The fact she was owned by Navratilova head to head in such lopsided fashion in the 80s when Evert was still close to her prime, eliminates her from being considered above Navratilova, and thus from any real consideration as the greatest ever in most peoples eyes. When you have two people that are contenders for the greatest ever, and that person is perceived to have "owned you", it is a bigger mark against you. In fairness to Evert she only trails the overall head to head 43-37, but the perception from their matches is that prime Navratilova completely owns prime Evert, fairly or unfairly.
For Federer it is still a mark at this point IMO, but not as much as if Nadal was a greatest ever contender which he isnt even close to being, or will ever be realistically.