I can only answer based on the applications I've seen. When I see applicants from a school that does the GPA thing, I've noticed these transcripts show a cumulative GPA AS WELL AS a GPA listed at the end of each year (which is not cumulative, but only a score of that year). When we come across these applicants, we without a doubt look right to the Clinical Grades unless something about the Basic Science grades draws our eyes back up there.
In fact, we had an applicant that had a GPA decrease in each year (4.0 after MS1, 3.6 during MS2, then 3.2 in MS3) and we basically tossed the application. His transcript listed his class rank at the end of each year as well. So, even though his basic science grades were a 3.8 (top 8 in his class) his MS3 grades were so subpar that (1) he wasnt AOA and (2) we were no longer impressed by him. Again, this is just one situation, but I think it can be translated well.
Again, however the overall GPA (and AOA status) depends on all the grades as a whole...so dont ignore them...but do NOT focus your whole application on them.