This is total bollocks. First: what's the great tradition you're referring to? The one where King's 1sts play Grammar's 3rds? Yep, that's a beauty. How easy is it to schedule games when all the GPS schools field different numbers of teams? The whole point of the mooted tiering structure is that the first criterion you would apply would be the number of teams fielded each Saturday. So schools who can field, say, 25 teams will play other schools who can play 25 teams and schools that can field 7 teams will play other schools that can field 7 teams. And obviously you'll never get perfect match-ups, but this is a better start than the position that exists at the moment. If, say, Knox and Waverley meet that criterion, then they have more of a place in a top tier than, say, Grammar or High.
There's nothing very hard to understand about this.