Let's clear up a few things.
The Plume Shield was donated in 1930. There was a competition table, points awarded, trophy awarded, the whole nine yards. After 1941, the competition was discontinued. The view was taken that it was unseemly to have a sporting competition conducted during wartime. Matches were played, of couse, but it was stressed that there was no official competition. Of course, everyone knew who had won the most games, and that school would then claim to be the "unofficial premiers".
This state of affairs existed until 1988 (or 1989 - I'm not entirely sure). Then it was decided that the Plume Shield competition would be revived, and an "official" premiership was contested for the first time since 1941. At some stage, some bright spark decided to go back and add all of the "unofficial premiers" to the list of winners. No doubt this was well-intentioned, but it was dumb, because it involved imposing on the competition, retrospectively, a set of assumptions that did not exist at the time. To give only one example, what about the years when the title was shared (my favourite, by the way, is 1972, when four schools won three games and lost two). Had there been an official competition then, would the winners have been decided by bonus points, for and against, some other method, or would the title have been shared? No-one can say, because there was no official competition, so no-one worried about it.
In the same way, no-one bothered to clarify the impact of the St Pat's games, and this created chaos. (The St Pius games caused less trouble, because pretty much everyone beat St Pius.)
Take 1979. If my memory serves (and I am, remember, a cartoon pig, so I can't be trusted entirely), in 1979 Waverley beat everyone except St Pat's and Trinity (a 14-14 draw - I do remember that one). St Aloysius lost to Waverley but also beat St Pat's. So if you counted St Pat's and St Pius, St Aloysius had won 6 and lost 1, to Waverley's 5 wins, a loss and a draw. If you include only full member schools, Waverley's four wins and a draw beat St Aloysius' four wins. Both schools claimed the premiership that year, and no-one bothered to sort it out, because it was "unofficial" - it didn't really exist. I would say that as a general rule, teams that beat St Pat's said that the games counted and teams who lost said they didn't.
Perhaps one area where St Pats were treated poorly in this period was that its players weren't eligible for CAS teams. I suppose that no school wanted to reduce the prospect of its own players getting a run.
St Pat's, I should add, had some handy players in this period. Danny Naylor was probably one of the best - a loose forward who made it into the Sydney senior team at one point, I think. The 1980 team was a strong one, with Naylor, Tony Cox (who was a reserve fly-half for the NSW Schools 2nd XV that year), and Roger Harkin, who went on to play quite a bit of First Grade at Sydney University. And of course Michael Foley came through in about 1984. St Pat's would have been really formidable in the early 80s (say 80-81) had they been able to reach an understanding with the Gales, Scott and Brett. They wanted to combine playing League with their school football, and the school couldn't accommodate that, so they packed off to Holy Cross Ryde and League. They really were superbly gifted schoolboy footballers, although life didn't turn out well for either of them, as Scott died sadly young from motor neurone disease, and Brett ended up doing time for his part in an armed robbery.
End of history lesson.