I just happened to be looking over the Connex Website when I noticed a new section for "Rail Enthusiast Permits".
The gist of it is that the new system allows an amateur photographer to apply for a three-month "Rail Enthusiasts Photography Permit - Suburban Stations" which will allow him or her to take photographs of trains at any Connex station.
However, the permit does not apply at a number of nominated major stations. These stations are: Flinders Street, Spencer Street, North Melbourne, Richmond, South Yarra, Caulfield, Camberwell, Footscray, Clifton Hill, Box Hill, Dandenong and Ringwood.
A specific permit is required for each station with this Rail Enthusiasts Photography Permit - Major Stations valid for one week at a time.
Note that photography is still banned outright in the loop. Also, Spencer Street Station requires a separate pass from the Spencer Street Station Authority.
The form for stations not listed as "Major" is here (PDF):
And the "Major" one is here (PDF):