We have to remember that this is basically a youth league, and just like every youth league (including Little League Baseball) there are rules that help the game be fun for everyone who plays. Scoring caps for innings/quarters/periods/halves (depending on the sport), inclusion rules where every kid on the team has to play for a minimum amount of time (or innings, in baseball), and yes, even these less-used rules limiting certain players. It's all in the spirit of sportsmanship, because a kid whose team loses all their games and gets blown out consistently, or who doesn't get to play because they're the worst on the team, will just want to quit.
There are more competitive leagues and tournament leagues that focus more on winning than on sportsmanship and a fun environment - those can have whatever rules they choose - that this sixth grader could play on if he chose, where he wouldn't be held back and by all accounts would be subjected to a higher level of competition. But in this youth football league the focus is on playing the sport in a way that makes the game fun, but aims not to give one team too much of an advantage or disadvantage, and that's perfectly fine.