1. Alto isnt touching the lakeshore or any other routes. Least not yet (cue Tor-Ldn phase 2 fantasy maps)
2. Air canada wants to get off the short flights that they lose money on. and they can implement exclusive connections via Alto
3. id expect a premium if i was to get there 50% faster. were looking at $50 for Toronto to Ottawa for lakeshore route. I wouldnt be suprised at 3x the cost
Alto cannot touch the Kingston sub, it is CN property and the Carney government publicly stated they were not going to expropriate CN property.
I would argue the fact that Air Canada is part of the consortium suggests one of two things;
1) AC will influence the price of Alto to offset the perceived loss of revenue of the short haul flights vs long hauls(i.e. influence the Alto ticket price above their flights)
or
2) AC will do as you say and flush the short flights in the Montreal-Ottawa-Toronto triangle to Alto by influencing pricing favorably in Alto favor.
When it comes to Air Canada having a conflict of interest, I'm a bit of a cynic. Canadian industry/business loves oligarchies. Look at our telecommunication plans, the bread scandal involving all the major grocers. It would not surprise me at all if Air Canada goes option 1; price Alto higher then their short haul flights.
Keep in mind, unless things change (which they can) Dorval airport is not being served by Alto in phase 1 (Ott-Mtl). The REM will be calling at the airport(Dorval)and the consortium will probably ensure Alto connects with the REM network somewhere in town(Montreal). Pearson is in the same boat, there's nothing so far to suggest Alto will stop there. Should Toronto Union not be the stop in Toronto, UPX cannot ferry passengers to and from Alto.
Considering, the Mount-Royal tunnel was only recently converted, I do not believe a secondary tunnel under the mountain will be built. Public transit(Metro) most likely would link anyone looking to use the REM from Central station to head out to Dorval airport.