I'd like to hear your explination (physical constraints aside i.e. grades) as to why the twisted track alignment could not be done. I've never heard this argument be presented in all the documentation that I've read about the wye.
Because the system was originally designed for integrated operation during rush hours only; at other times upper St. George and lower Bay needed to be configured to operate as alternating stub terminals for Yonge-University.
The University tracks at St. George were specifically placed on the upper level as insurance so that the University line could be extended north or connected into the Spadina line if integration didn't work.
Also, grade separation. The distance between Bay and St. George did not allow sufficient clearance for a twisted arrangement ... plus increased cost and complexity, etc.
So it WAS carefully designed by the same guy who designed the Greenwood wye, which is laid out differently. He could have applied the Greenwood design to the Avenue Road wye, but didn't, because the double platforms also served as holding points for the trains before they merged. However, he didn't extend the concept to Museum, and so trains were usually held in the tunnels before they merged into Museum Stn.
I rode the integrated system and I know all of its internal workings. All of the signals were on rigid timers, controlled by what they called automatic train despatchers. This system didn't work because trains couldn't stick to the strict schedule, so the wye was managed mostly on an impromptu basis by human hands for the first six months ... to keep the trains moving. Even on Day 1, they had to hold trains above and beyond what the ATDs were doing so as to preserve the alternating service pattern.