I also heard that the plan is for 4 tracks west of Scarborough, but not that the Stouffville line gets its own pair. That would completely mess up the operation of the Lakeshore East and VIA services.
As far as I can tell, the current 3 tracks operate with the two outer tracks serving local trains and and the centre track serving express service in one direction (peak direction, or alternating at other times of the day). Some VIA services do use the local tracks, and they tend to be slower (i.e. stopping at Guildwood) in order to fit between the Lakeshore local services. Cutting off the express track at Scarborough would cause serious capacity and service flexibility issues.
The Stouffville trains make no stops along the corridor, so my best guess would be that the fourth track operates as express in the counter-peak direction, with peak-direction Stouffville trains sharing the express track with Lakeshore and VIA trains. A 5 track arrangement (2 Stouffville, 3 LSE/VIA) would be preferable, but I don't think there's room for 5 tracks, particularly around Danforth. I was surprised they thought they could even fit 4 tracks.
I don't think it is necessary to give VIA a specific track. From what I can tell, Metrolinx is quite reasonable to them and it would actually make matters worse to require inter-governmental co-ordination just to allow a train to switch tracks. Besides, outside of peak periods, they are the only ones using the centre track anyway (there aren't platforms at all stations so GO can't use it).