Can players in single-elimination rounds agree to split prizes unevenly?
You are referencing the wrong part of the MTR for you question the relevant part is a few paragraphs above that.


  Players are allowed to share prizes they have not yet received in the current tournament as they wish and may
  agree as such before or during their match, as long as any such sharing does not occur in exchange for any game
  or match result or the dropping of a player from the tournament. As an exception, players in the announced last
  round of the single-elimination portion of a tournament may agree to divide tournament prizes as they wish. In
  that case, one of the players at each table must agree to drop from the tournament. Players are then awarded prizes
  according to their resulting ranking. [MTR 5.2]


So what they are allowed to do is combine their prizes (4 + 1 in this case) and split them anyway they choose to, from 5-0 to 0-5 or anything in between. Then one of the 2 players drops from the tournament and they get their prizes and split them up as previously agreed.

The portion you quote is intended more for when you are in single elimination brackets, but you haven't gotten to the final 2 yet. For example at an FNM after 4 rounds of Swiss and a cut to Top 8, it is 1am and everyone wants to go home to sleep, as long as all the players and the TO agree they can stop the tournament there and split all of the prizes that would go to the Top 8 spots evenly between all of them. The rules do not state what happens if the prize payout in this case is not evenly divisible by the number of players.