For people who are interested, the preliminary design business case study that looked at the fly-over option closely was way back in 2011, but you can still access it:
https://assets.metrolinx.com/image/...ner-Mid-Term-Service-Expansion-PDBC-FINAL.pdf
Hourly AD2W service was possibly without the flyover, but it would have prevented travel-time reductions to 90 minutes and made cascading delays more likely due to an additional train meet at Georgetown Station. It also added ~190 million to the cost of the line which they state was beyond the budget for the program.