It sounds like the OP just doesn't want his kid to be rated the "5". If he's missing a bunch of games, the team will be crushed as the 5 are typically the main goalscorers and it sounds like he just doesn't want the other kids to moan "oh little tommy's not here today....we're going to get crushed...we hate him because his club team is more important". It is absolutely true that balancing of teams is imperfect and there is absolutely funny business that goes on in creating things like super team. The said, most regions do give at least lip service to balancing. The main problem is that the ratings aren't particularly accurate. My son's second year (only played 2 years of core before doing extras), the coach of the team from the first year decided he was going to be nice, and since they won most of their games, rated every player a five, including one player with some handicapable issues. My son got assigned to the team where 3 of the players rated a 5 were rated, and where a second handicapable player (the coach's son) was also assigned (the coach's son not being in the draft). There's a cap in most regions on the number of 5s you can take....it was a disaster....my son rated a 4 and another kid rated a 4 were the two strongest players on the team and between them had maybe 10 goals all season (they also each had to do a stint in goal which took them off the field)....they lost every game except tied 1.
It seems the bigger issue, though, is the missing of games and missing supposedly of practices (since they'll conflict with club practices). I'm not a proponent of players getting extra play time in AYSO core, even if they are a bencher. The other players lose something by the missing player not being there in practice, and the swing in expectations makes it difficult for the coach to make a line up. At a certain point (when they move to 11v11) it will also start to drive the club player crazy. There was a father on here who advocated it would make his daughter a stronger player and leader, but IIRC it didn't work out that way. He did it right, however, and he agreed to coach, so the repercussions of this arrangement would be on him, and not some third party to figure out, especially since at the younger ages AYSO tends to limit the numbers they put on teams in order to maximize playtime (if 3 are out ill, on vacation, or playing in a club team, that's it and you are playing undermanned). Being the coach also works in that in most regions, if it's your kid, they aren't in the draft.