Say I want to end up a dental surgeon by taking the bio-medicine route (hopefully completing this degree at Melbourne Uni), how much a difference would it make to my future if I go Melbourne Uni (96 ATAR required) or say something like Deakin (83 ATAR required)?
I don't think Deakin has a dental school. I got pretty curious when I saw this but couldn't find any info on it 
La Trobe is the only uni that offers a 5 year undergrad entry dent in Victoria which is a 3 year health science course followed by a 2 year master of dentistry. The other school in Victoria is Unimelb which offers the 4 year graduate program.
The other dental course I can think of is USyd which is also a graduate-entry course.
All the courses are accredited and competitive in terms of entry so you shouldn't worry about one uni being more prestigious than the other 
No, I think he/she wants to know the difference between biomed at Melbourne and Deakin.
There really shouldn't be a difference when it comes to applying for the DDS at Melbourne. I have found, though, that there is better support in the Biomed pathway at Melbourne for aspiring doctors/dentists etc (even in comparison to Science at Melbourne) as the teaching staff have an expectation that the bulk of students in these courses, or at least from within Melbourne, will be from Biomed.
If you can't get into Melbourne, then you can still get into the DDS provided you fulfil the pre-requisite requirements, which can be found at
http://www.sc.mdhs.unimelb.edu.au/sites/studentcentre/files/Prerequisites_VIC_0.pdfAnd if you would rather be at Melbourne, you can always do science there instead of biomed at Deakin, and still qualify for entry into the DDS.