no it doesnt.
everyone at YOUR school will have done the same paper, so no one will be disadvantaged or vice versa.
i'll give an example.
school (a)
alan: 1st - 100%
alex: 2nd - 90%
allana: 3rd - 80%
school (b)
bob: 1st - 50%
brian: 2nd - 45%
bill: 3rd - 40%
now if school (a) students get marks x, y and z. consider that it is in order, mark for allan > alex > allana. they will get certain uai's.
if bob, brian and bill also get hsc marks of x, y and z. (again keeping the order, bob > brian > bill) then the same positions in the schools will have same uai's. allan = bob, alex = brian, etc.
you see how having a lower INTERNAL mark submitted to the board doesnt affect anything. the internal marks only determine your ranks, more importantly, relative differences between ranks.
hope that was clear enough...