Here's my assessment of what's happening. I'm just done with my Ph.D. application process and will be starting my studies this fall. This is strictly what I have observed. I don't have any objective data.
In general, it is true that, as you guessed, some artificially lower percentages for aceptance rate are shown, especially in mid-tier schools, which are often back-up schools for top candidates. Most candidates apply to at least 8-10 schools and when they get an admission from a top school, they withdraw their applications to lower ranked ones. Because the number of seats in each program is so small, (informal) waitlist plays a huge role. Say a typical department A receives 100 applicants for 3-4 seats (most admission processes are conducted by department, the school only comes in for administrative purpose in the beginning and once an applicant is admitted), they might put 20 shortlisted candidates and reject the rest. They usually make a shortlist within that shortlist and start contacting candidates for an interview and making offers. Typically, the remaining 15+ shortlisted candidates won't hear a word. Once candidates are offered an admission, they are usually pressured to accept it asap but most wait til 4/15, so the waiting game for other cnadidates is long and frustrating. This is especially true for mid-tier schools which receive applications from very good candidates but those same candidates are often waiting for a decision from top schools. Depending on whether their first admitted students accept or reject their offers, the committee goes down on the shortlist and make additional offers. At this time, many actually assess probability whether a particular cnadidate would come if an offer is made. Therefore, if a particular candidate already has an offer from a "better" school as it'd be meaningless to extend an offer. What I just described is typical but very different across schools and even dependent on each professor's personality.
I believe low GMAt/GPA can be deal breakers but they aren't deal makers. They are normally used to pre-screen candidates but once you're on the shortlist, you're selected based on your recommendation, SOP and interview results. A typical 650/3.5 won't get an admission from respected programs but a 750/3.8 won't guarantee you an admission. Obviously, fit plays an important role as professors look for candidates they can work with for their own research agenda.