As it stands now, GO is on the south side around the Humber River to the cut off and on the north side for rest of the route to Milton. There has been a plan from day one to have a GO fly under at the Humber area. Between the fly under on GO on opposite side of CP Mainline that will have 2 + 2 tracks in the corridor, there is nothing stopping the line being electrify other than the Streetsville area yard and cut off. To deal with that area, you will need to build 2 more fly under to have the GO tracks on the south side starting at the 403 and then west of the Meadowvale station. This mean rebuilding the Meadowvale station with a centre platform and a side one.
CP has seen that 4 track corridor as having 3 tracks to use when needed than their current 1-2 tracks. If you really want to please CP and have electrify tracks, you build 5 track where it can be done and there are areas you can do it.
As for a branch Line to Sq One, you use a tram-train that connect to the Hurontario Line that only needs a short section area to do it and it is there now.
At some point, Mississauga Rd has to be grade separated as well 2 others and the closure of 2. 9th line is already on Mississauga books to be grade separated and this leave Halton to grade a number of crossing. To do all of this is close to $3B compare to the $2.1B plan in 2014 that only had one fly under, 4 tracks and no grade separation.
CN Halton sub can support 4 tracks compare to the current 1-3 tracks in place now, but getting CN to do the same thing as CP could be easier, but still costly to do. Then there is the double tracking the line to KW that has its own issues with many grade crossing.
Once there are battery power trains, then the electrifying the line is a non existing issue. Still need areas to charge the battery power trains along the route as backup service.
As I stated in the past, there is no missing link that others call it it, but and other than a new route that has to be paid 100% by the province since it their call to do it. It will be build to RR standards, but provision must be made to allow HSR type service on it for future needs. Can see the Halton Sub to Burlington and to the east of Toronto having RER type service on it.
There is no needs for stations at Sherbourne and only haft the stations for Cherry St as well at Spadina.