The advanced degree is essentially the same as the standard Biomedical Science degree, except in third year one of your electives has to be a research elective, and of course there is an honours year included. I think there's also an opportunity to participate in an extracurricular program (not too sure on the details). I believe its relatively easy to move from an advanced degree into the standard degree.
Are you referring to the biomedical sciences pathway to graduate medicine at Monash? If so, you are still eligible for the 50 places. Should you be offered a place (and you are doing the advanced course), you can either defer your offer for a year (while you complete your honours), or forgo the honours year entirely.
In general, you can still use the degree to apply for medicine at other universities (as you would with the standard degree). Note that some universities (not Monash) also consider honours years in your application.