Welcome to MSO and congrats! 
I can't comment too much on the details of each of those courses, but just my 2c on a few things.
For someone such as yourself who did exceptionally well in school (I'm assuming 99.95), maintaining that average is not going to be an issue. Yes, uni is different and some people do struggle with the transition, but 65 is certainly not a tall order for a BSci.
Prestige doesn't matter. The way NSW allocates internships is essentially random, so they don't look at your uni. After internship, I don't think anyone would make more than a passing glance at your tertiary background either.
So to bluntly answer: Would that make a difference in the future as a doctor? No.
I can't comment too much on the details of each of those courses, but just my 2c on a few things.
Also, I understand that I need to maintain a D average and WAM of 65 at USYD to continue into medicine. Could I get a measure as to how hard that really is?
For someone such as yourself who did exceptionally well in school (I'm assuming 99.95), maintaining that average is not going to be an issue. Yes, uni is different and some people do struggle with the transition, but 65 is certainly not a tall order for a BSci.
Another thing, I have also heard (it is not my belief) that USYD is much more prestigious with a better reputation. Would that make a difference in the future as a doctor?
Prestige doesn't matter. The way NSW allocates internships is essentially random, so they don't look at your uni. After internship, I don't think anyone would make more than a passing glance at your tertiary background either.
So to bluntly answer: Would that make a difference in the future as a doctor? No.