That Chart was new in 2013-2014 and is used by AMCAS to classify applicants. "Disadvantaged" is an applicant's self- classification, separate from parents' SES. There are cases where one might have grown up poor despite not being in E1 or E2, for example if a parent with high educational attainment was disabled and unemployed for many years. More typically, the "disadvantaged" applicant is born to a single mom and raised in poverty, sometimes ending up in the foster care system for a time or cared for by relatives if mom isn't around or is irresponsible.
I have seen adcom members who have been very negative toward an applicant who they felt was inaccurately claiming to be disadvantaged.
If you think that you were at a disadvantage in terms of preparation for college based on your life circumstances from 0-18, then consider checking the box. Otherwise, know that AMCAS will classify you and you need not claim disadvantaged status to draw attention to your childhood circumstances.