VLine can just terminate Gippy trains at Flinders St like they used to, no need for flyovers, just give them Platforms 6 and 7 permanently once the metro tunnel opens, the crossovers are already there.
Outside of peak you can do stock transfers if needed for cleaning, fuelling, maintenance.
edit: Like this,
Platform 1: Clifton Loop
Platform 2: Burnley Loop
Platform 3: Burnley Local (Turnback)
Platform 4: Burnley Local (Turnback)
Platform 5: Northern Loop
Platform 6: VLine (Turnback)
Platform 7: Caulfield Loop
Platform 8: Cross City towards Frankston
Platform 9: Cross City towards Newport
Platform 10: Sandringham (Turnback)
Platform 12/13: Sandringham (Turnback)
The loop lines only need one platform, Metro needs to timetable away from stopping trains at Flinders St for changeover. Clifton Loop already does changeover at Clifton Hill, need to look for similar at Caulfield+Burnley+North Melbourne/Footscray for the other lines.
The turnback lines have two platforms becuase of the crossover conflict, so need more space for timetable recovery.
Ideally, Upfield and potentially Craigieburn would terminate at Spencer St platforms 8/8s to free up space and remove the number of lines in the northern loop.