As far as I know the CASA recommended syllabus does not say "high level flight required above YMML in order to obtain PPL CTA endorsement."
I've flown over YMML probably more than 30 times and I don't think I've ever been given a heading or level change unless I've requested it, except for descent. That argument is moot. You've got me wondering how you can be assured of getting a heading or altitude change other than asking and if schools are doing that I'm not surprised that ATC are denying transit clearances.
Flying into and out of Essendon is a far more valuable experience for the student than a VFR transit over YMML will ever give. If it is an actual requirement of the school then do it over Moorabbin, it's still class C. My last AFR took me through class C over Moorabbin, nowhere near YMML.
TNIP - I know how syllabuses work; I wrote a Nav syllabus for a flying school. I chose the routes and distances and they did not include "flying overhead YMML."