Romo had the better supporting cast (better OL, average run game, less terrible defense) putting him in a generally better situation, fewer yards, and a lower Y/A. The vast majority of film study cats from that season put Eli > Romo.
If you switched them, the Giants weren't winning that division that year (though Dallas wouldn't be winning the SB either; that ridiculous defensive turn around late the Giants had wouldn't have transferred the same way).
I just think it's a pointless point.
"Oh, you're not one of the absolute unquestionable GOATs, so let's act like you aren't exactly what every team that drafts a QB high could realistically hope for and that you didn't have great careers in your own right." Nah.
And while Brees is great, above them, he shouldn't be mentioned with Brady, Rodgers or the sexual assaulter either.