This. I had 1 interviewer who was immediately hostile out the gates, and jumped down my throat very time I opened my mouth. I also had people that seemed sympathetic. It really is subjective and depends on who reads your app. Just try and stay moderate in your explanation. I think mainly the Republican minded people take offense to it. Nothing you can do about it, just try and toe the line.
I had a similar experience at one school: they asked me since I was disadvantaged, how I afforded to study abroad and volunteer internationally (along with pointing out every other potential red flag on my application). Worst interview experience ever, but I ended up getting accepted so I guess they must've liked my answers. Several other schools asked me about it and I think it did indeed help me show my motivation, perseverance, and resiliency in the face of adversity.
You should mark disadvantaged because it provides the admissions committee more context and background about who you are and the experiences surrounding that, things that you may not even see. It will definitely show that you've overcome more challenges, shown resiliency in the face of adversity, and less enrichment opportunities that the privileged class don't specifically realize the "disadvantaged" class don't have. I'm not saying that people who don't check mark this box haven't overcome their own set of challenges and difficulties in their lives, but just different kinds that might have some sort of historical significance. It'll allow you to provide extra information on the context behind your motivation and your maturity, which I believe definitely does help schools learn more about why they should be impressed with you.
Marking this box puts you at a different baseline than those who don't check it off, which allows admissions committee to see the progress of your career development as a future physician. That's not to say that they will accept you if you're missing critical items in your application (shadowing, volunteering, research, ECs or other doctor-affirming activities), but they'll see how these opportunities might not have come as easy as those who don't have this box marked off.
For what it's worth, I applied with disadvantaged status because I was raised by a single mom with a mental illness on a salary of government supplemental security income (about $13k/yr) since 6th grade. I checked that box off, had below average GPA but above average MCAT, received 16 interviews and 3 acceptances. Don't feel guilty if your struggles aren't as "profound" as the next person because in the end, if you qualify for what they define as "disadvantaged," you should indicate it as such on your application.
Again, this is my opinion and I hope there wasn't anything that offended anyone in my post. Most of these points can probably be highly debated or even controversial, but it's to your advantage to have these debates and be acknowledge these issues during this application cycle to increase your self-awareness on where you stand as an applicant.