I'm just enough of a conspiracy theorist to wonder whether the original GO Expansion plans for LSE and Stouffville were quietly rewritten when Ford launched the Ontario Line idea.... and maybe again when Ottawa began to look (marginally) sincere about Alto.
As I watch the Ontario Line construction zoom along, it sure looks like restoring that third track can't happen until the OL work is close to completion. Too much physical encroachment to do otherwise.
Similarly, if some form of passenger rail along the CP Belleville Sub emerges, there may need to be new designs for the CP overpass in Agincourt, with or without a connection of the trackages, and whether or not Alto goes up the Don or via Scarborough Jct. So maybe the Stouffville line, which was an early-start project originally, is now in wait-and-see mode.
That change in priorities may be a very rational and wise decision from cost and construction logistical perspectives...but if true it's a confession that ML may be sidestepping.