It's not going to be separated out. Just like it makes no sense to separate BY and SY at scale when comparing team ratings, it makes even less sense to separate just MLSN1 teams as it's the only one in BY anyway. The overarching point (and the pragmatic one) can always be that MLSN1 and the ratings of its teams > every other league, way, way more than RAE > (RAE - 5 months). If MLS1 gets put with the older group, they are still going to make up virtually all of the top rankings. If MLS1 were pushed in to the younger group, they would still make up virtually all of the top rankings, even more so than today.
ECNL and its teams are never going to be able to show greater (in SR) than MLS1 in any circumstance, until ECNL teams start performing better than MLS1 teams - and it doesn't look like that's happening any time soon. They can't expect to be able to call themselves fake #1 because an app chooses to not compare them to other teams in that age bracket that outperform them. It's like a GA team saying that they are national #1 (except for the ECNL teams).