I think (not 100% sure) that unis do see your ATAR, but they will automatically apply their adjustments when considering offers e.g. SEAS and subject bonuses, where applicable. As far as I know, the only real thing the institutes consider is your selection rank when ranking everyone for offers.
If you have received the lowest ATAR but miss out on the lowest selection rank for your cohort, then it becomes less likely that you’ll receive an offer as you’re deemed less competitive, but you might be considered in later rounds assuming you’ve got said course as a higher preference than you’ve been previously offered.
As for “will you still get in?”, it depends on how many spots are left, how many people are vying for it (still want that course according to preferences) and how competitive you are. Since this isn’t made public, you won’t know until you get offered (or are unsuccessful in all rounds) if you’ll get in or not.