DO schools do not have larger deposits because they get less funding. It's because DO schools are frequently used a backup to MD schools, and people traditionally held many DO acceptances until they got an MD acceptance, then dropped the DO acceptances, leaving those schools to open up to the waitlisters - usually at the last minute, causing lots of grief and stressful decisions. Wasn't unheard of for someone about to matriculate to a DO school, then withdrawing to go to an MD school come May 15 - or just before school started. The DO schools required larger deposits to discourage this.
The high deposit is meant to make it harder for someone to hold multiple acceptances. I mean, can you really afford to drop $5-6K in deposits to multiple schools? It's meant for you to seriously consider whether you want to go to the school or not, because as they make plainly clear, once you send that deposit in, it's non-refundable.
Lots of students face this problem early in the application year, when they get accepted to one school that requires a large deposit while waiting for other schools to either admit, waitlist or reject. Conventional wisdom is that if you have no other acceptances, and the window to accept with a deposit is closing, to suck it up and place a deposit on that one school and see what else shakes out the rest of the interview season, with the understanding that that deposit was lost and the cost of playing the med school admissions game.
It's not every DO school that does this, either. TUCOM, when I was applying, was the harshest, with a $2000 non-refundable deposit requirement two weeks after acceptance. If you interviewed early there and were accepted, you had a tough decision to make. Western, like other schools, require the deposit in two steps as time passed. Some state DO schools do not require a high deposit and are line with a lot of MD schools.
Another reason why MD schools have lower tuition deposits is that traditionally students wait for the financial aid packages from each school, which could drastically change the affordability of each school. DO schools don't give nearly as much fin aid, so holding on to mutliple acceptances with the hope of getting aid isn't as important.
With the MD schools, the fin aid package can make an expensive school much more attainable, so they make it cheaper to hold on to multiple acceptances until May 15, when you are required to keep only one acceptance. Can't do that if you have drop a grand at each school. So, in reality, the MD schools aren't doing this because they're better or nicer, but as a method to keep you interested in their school and not scare you off right off the bat with their listed tuitions.
Things to think about.