I think it depends on the specific part of the facility.
Weight room, hydrotherapy rooms, training rooms, classroom, discipline rooms, etc: I see no reason that the organization would not open those up completely to the minor leaguers when the MLB team is not also there. It would be a terrible waste of resources not to.
2,700 square foot Major league clubhouse: that one will probably be MLB players only, year round.
MLB dining facility: This exists because the MLB players expect to eat a heck of a lot better than the minor league players. It might just get repurposed into a second general cafeteria when the full MLB team is not there. Like, the team chefs may travel back to Toronto with the team anyway?
Barber shop: who knows, maybe that's a little MLB player perk