Whether you share tracks or platforms with GO/RER, every intercity train you operate is at least one train less they can operate. Even if ALTO trains should be much more on-time than VIA trains today, I would still assume that they would (at least when heading towards Union) be inserted ad-hoc (rather than with a dedicated slot), slightly delaying the following trains until the headway buffers stabilize the timetable. I could be wrong, but I suspect that if you go more frequently than twice per hour, too many suburban/regional trains will be affected.
Or maybe a different example: If you actually schedule the intercity trains, you would define a slot every 15 minutes (because all other trains operate every 15 minutes or multiples of that). If you operate the intercity trains every 30 or 60 minutes, you always have a free slot 15 minutes later, which you can use if you arrive late. If you operate more frequently than that, you would no longer have that luxury…