Relieving drivers doesn't take seven minutes - if there is a source for that idea then it isn't very credible. Generally the miniumum preferred at Flinders Street is two minutes - and dwell time at Flinders Street is primarily dictated by other timetable requirements, rather than time for crew changes.
Drivers are also relieved mid-journey at other locations on the network where they sign on and off - such as Carrum, Mordialloc, Dandenong, Westall, Macleod, Eltham, Broadmeadows, Ringwood and Upper Ferntree Gully. There is no time allowed in the timetable for when this occurs.
There are advantages in relieving all trips at Flinders Street - primarily making it easier for trains to be transposed without causing a driver to necessarily be out of position. However, it is principally driven by industrial agreements - especially the requirement that (with some exceptions for shuttles) drivers do not operate more than one out and back trip on any line during a shift - eg a driver can only do one trip to Sandringham in a shift.
I don't think that changing drivers at Flinders Street is an essential part of Melbourne's system - but I think its impact on performance and capacity is negligble and it certainly has advantages to go with the disadvantages.
The negative impact on timetabling the system caused by relieving at Flinders Street is overstated by some 'experts', whose principal expertise is coming up with something, anything, that is different. Most groups have more than one platform for arrivals, so pumping trains through Flinders Street at high frequencies could theoretically be handled whilst continuing to relieve there - but its the infrastructure constraints on the rest of the network which really constrain the timetable. If the aim is to improve productivity of drivers - that is a whole different debate - but comes with its own set of complications.
Meanwhile - back to simplifying the timetable - so long as you have a system of many flat junctions, single line sections on 8 of the 15 electrified lines, the old fashioned pleasures of such museum pieces as staff and ticket (not for long though), the need to balance shorter journey times for outer suburban journeys against frequency on the inner network, lengthy lines mixing non stop V/Line services amongst a suburban service, a complicated fleet maintenance regime generated by a huge number of stabling locations with decentralised maintenance facilities, an overcrowded network where stopping patterns are juggled to shoe-horn excess passengers onto any bit of fresh air left in the peaks etc etc, you are going to have a complicated timetable.