Just to add to what
@smallspy said above, here's an aerial pic of the former yard;
View attachment 401885
This is a close-up just west of Millwood, the active rails are the current CP mainline:
View attachment 401886
This is closer to Bayview, you can see a single track to the south (right) of the yard area in a sort of gully or ditch as it descends to go under Bayview Avenue, that track connects (non-operating) to the Metrolinx-owned
track in the valley.
I don't have any official reasons as it pertains to the GO layover function, but informally, I'm under the impression there was a desire to avoid the cost of rebuilding the 1/2 mile bridge in the near-term. I never asked about the site as an Ontario Line layover; also, Mx doesn't own the yard lands, so would have to negotiate a purchase, I believe they thought the valley option would be cheaper and faster to deliver; but I am surmising that.