Maybe Alto is part of the reason they're in no hurry to get the Highland Creek bridge unstuck, given that that's the location where Alto would be joining the corridor. But I don't think Alto can be an excuse to delay the other projects in the pipeline. The Mount Joy second platform is necessary to extend half-hourly service north of Unionville, which makes no difference to Alto since they won't use that part of the corridor. The second platform at Kennedy is just an extension of the existing double-track segment that GO uses for 30-minute service during peak periods. So its benefit is primarily a speed and reliability improvement for existing services, not an increase in frequency. The latest "
mission" for the Stouffville line is only 4 trains per hour between Unionville and Union, so I don't think there'd be any need to build any additional tracks for Alto at Kennedy. All trains would stop there so there's no need for an overtaking opportunity.
Maybe having intercity trains on Stouffville between Highland Creek and Union would affect their decision to delete the Scarbrough Junction rail-to-rail grade separation, to let Alto trains access the express tracks on the quad-tracked segment between Scarborough Junction and Union. But I doubt it. Unless the feds force them to play nice with Alto, Metrolinx would presumably just do what they do to Via and make Alto trains plod along behind GO local trains on the same track.
Here's a conceptual layout I made back in the HFR days, but I think it would still apply to Alto. The main difference compared to the current plans is that Scarborough station is on the Lakeshore East local service rather than the Stouffville line, to minimize the speed differential between Stouffville line trains and intercity trains.
There would also be non-revenue track connections not shown on the map. Obviously the quad-track segment at Lawrence east is only required if they build that station.