In that case, assuming that all roads will be of freeway standard, MTO will need to take over City Road 55, 34 and Maley Drive.

Nobody coming from west of Sudbury to North Bay or further east will use SE Bypass anymore, in that case.
Of course, the City of Greater Sudbury can just do what T Bay’s doing - keeping trucks off “city roads” and on TCH, or what Windsor did - refusing to let MTO take back EC Row (blame Mike Harris) or merge the 401 extension with Highway 3 and EC Row.
Ps: Speaking of 401 extension, I still find it insensible that it doesn’t just merge with Highway 3. I remember North 42 telling me that people fought hard to take off the the table the option to merge 401 with EC Row.