How/where would the Sheppard line go above ground, though, and what routes would it follow to the west/east?
I think the options for above ground are mostly in the 401 corridor, and using that corridor makes sense for the outer sections only. We don't want to lose the density opportunities in the middle.
In the west, I'd suggest going mostly underground until Allen Rd; the West Don crossing may be on a bridge though because the valley is very deep. After connecting to Line 1 Sheppard West station, the line can turn south and continue at the surface level from Sheppard to Wilson. There is still unused space on the west side of Allen Rd to add a pair of tracks on surface, as well as to expand the Downsview subway yard, or build a new yard for the mid capacity (Ontario Line type) rolling stock.
Then the line would continue underground under Wilson till the Weston Rd / Albion Rd interchange. After that, the line can switch to the 401 / 409 corridor running at/above ground. If Pearson is the destination, then it can run there above ground entirely. If we want the whole line or a branch to continue into Brampton, then it will need to go underground again at some point.
In the east, the line would continue under Sheppard until at least the Agincourt GO station. Then it needs to connect to SSE either at McCowan & Sheppard or at Scarborough Centre, and then serve the Centennial College Progress campus; that section of the route is up to debate.
East of the Centennial campus, the line would switch to the 401 corridor at/above ground. Maybe, not even divert to serve UTSC directly, but instead have a station over 401 & Morningside connecting to the LRT that will run on Morningside and serve UTSC. And then it can continue in the 401 corridor all the way to Pickering GO Stn.