You are absolutely correct: AMCAS does not check ( at least not fully yet; more on that later )
It is checked by the actual medical school you have been accepted to at post admissions/pre matriculation step.
Every medical school requires each student submit official transcripts for direct check of academic records, proof of degree earned, fulfillment of prerequisites, etc. Typically this will include .... wait for it.... a National Student Clearing House report. In addition, virtually every student will file FASFA form and get report from DOE will include student loans records for undergraduate institutions, which will show what schools you have attended. So it would popup that point, after you have been accepted, which would lead to a probable withdrawal of that acceptance and unlikely ever being accepted again at MD or DO
And soon, AMCAS will in fact be checking it as it has officially partnered with .... wait for it... the National Student Clearing House for transcripts soon to be the only method for submission of these documents.
http://www.studentclearinghouse.org/about/media_center/press_releases/files/release_2013-11-06.pdf