Difficult to say
Talking about career pathways post graduation, it would depend whether or not the melbourne course offers a chance for research. Being involved in research is a good thing to have on your CV when applying to specialist colleges.
However as melbourne and monash have seperate hospitals it's likely that there will be little difference between the acceptance to postgraduate pathways as i beleive the hospital makes recommendations for applicants to the relevant training college for the training spots available at that hospital
USyd and UNSW have the same relationship. USyd is exclusively graduate yet both schools thrive and produce outstanding doctors, with each course having evolved to give it's own experiences and advantages
But for the most part it's too early to tell, the main advantage of the melbourne model is that you have the opoortunity to be exposed to the medical profession before you take med and can therefore decide if you like it or not, with monash you'll graduate a couple of years earlier, which is nothing really in the long run