How is that even possible? Canon with no supporting material is... not Canon? Home-brew? Unable to be complied with?... I don't see a choice here. Either a thing is Canon or it's not.
Canon is only vital to writers of future published material. To a Referee, Canon is just a designation for universally familiar elements.
This could be read as "Canon is irrelevant."
To a Referee, it CAN BE irrelevant. The Campaign at the table should ALWAYS be the priority. If Canonicity helps the campaign design and player immersion, GREAT! If the body of Canon helps inform a decision that isn't specifically outlined, and that decision doesn't disrupt the Canon
everyone is using at the table, EVEN BETTER. That's what "Canon Compliant" means.
In this case, there is little said directly about the internal structure of Psionics Institutes, and the few bits we have across all editions are different. To some, that leads to a crisis of Canon. To others, that says something else: "Published Canon says these institutes are not all the same, so I can make the one I'll be using different as well."
Canon is also, like the old saw about politics, *local*. If my campaign is in the Marches, the Canon regarding modern events in Diaspora is indeed irrelevant, and the Canonical list of historical events there is probably 99.9% irrelevant. Who cares how the Institute on Terra is run? I'm in Deneb! Years of travel away across an Imperium that is Canonically diverse. Terra's Institute is one example within that diversity, not a cookie cutter for every Institute everywhere.
And if you, the Referee, decide that Institutes in the 1100s are, in fact, all or mostly alike, you are still Canon compliant because Canon
doesn't say anything. AND you've now implied a new Secret for the players to discover. After three centuries of scattering into hiding on diverse worlds, why are they all still so alike? If that answer doesn't invalidate the Canon in use at the table, then even this is Canon compliant.