Outside of history, what are the reasons/benefits to continue with the conference structure in NFL? Under the current structure, it is impossible for there to be a Superbowl between the two best teams if they are from the same conference. (Yes, a similar question can be asked for the NBA, MBL & NHL).
This has A LOT to do with history, specially to the format and set up of the major league sports in North America. Let's compare the North American leagues to European Soccer leagues. In North America there is no promotion and relegation, and also there is only 1 cup per year. These differences result in having divisions and conferences to promote rivalry, and also indirectly to other phenomenon like the draft (that's not to say divisions are a strictly North American structure). Since the teams don't change, and there's only 1 championship to be won, a fair way to create rivalries is via the introduction of divisions and conferences. In most cases however, including for the NFL, these conferences came to existence in a very natural way of 2 leagues merging together. Rivalries are good for the leagues. It creates more anticipated match ups, which results in more fan and media attention, and so revenue.
Since in the other 3 leagues at least 82 games are played per season, one could argue that the conferences could be dropped, since each team can play the others' at least 2 times with a few more divisional games. Or perhaps with addition of a few more games to a season, all teams could play each other 3 times.
But that argument can't hold for the NFL. This is because as of 2021, each NFL team plays only 16 regular season games, while there are 32 teams in the league. Generally speaking, football seasons consist of relatively low number of matches per season. If conferences were to be removed, teams should play the exact same, or very similar number of games across their opponents. But in an NFL season one team can play roughly half of the other teams in the league at the very most. So the schedule parity would be very low to have no conferences in the NFL. Unless the games per season are at least doubled, which requires a drastic change of training, compensation, player intensity, and perhaps game duration, the NFL won't drop its conferences. Perhaps we're even more likely to see more conferences in the future, than their removal.
You should remember that the reason for the Superbowl, and the NFL's structure, do not exist for the purpose of "finding the best team", not to mention "finding the best matchup for the Superbowl". Even if they were, they'd likely fail no matter what - the NFL is the least likely sport of the 4 major sports to find the "best" team with its championship, mostly due to the one-and-done nature of the games.
The NFL's purpose is to make money, and the divisions and conferences enable this. Division rivalries lead to teams "hating" each other, and they play twice a season in-division; in-conference, they also play more often (they play six of the 12 in-conference teams each season, and every team at least once every three seasons, versus four of the 16 out-of-conference teams).
It's certainly possible to change this over time, but I don't expect it to change soon - even if they decided the divisions/conferences didn't make them money, any change tends to be disliked by a vocal group; there aren't a ton of people pushing for this, as opposed to (say) NBA playoff realignment (and note that the NBA still has divisions and conferences, and even in the playoffs the conference alignment still exists).