Well, I'm from MAPSS. just graduated from it last August. Though I'm in sociology not history, I do know couple history people.
For your question, yes, different people get different funding. I knew a history guy went there for free. I knew a soc girl went there for 1/3 tuition. I get none.... (let's skip this.) For detail funding, you probably have to look at your own package.
Overall I think the experience in MAPSS varies. I was lucky enough to have really good thesis advisor and other good mentors. I'm in the application process, so far I got one admission from Wisconsin (though w/o funding.) But I also heard tragic story like irresponsible advisors or huge pressure because of the super heave pressure both from the program and from the school. I can only say be sure to talk to people and get info before you choose your advisor and planned well. Chicago professor can be really self-absorbed and totally forget about you, esp. you are just as MA student.
I think the program furthers my chance for application and so far I hear good record for application from last year cohort. According to the stats MAPSS sent us last April, the application result for history, 2009-10 academic year: four out of five applicants got funded offers, the left one was on wait list for a school when they sent us the result stats. And the schools that made offers included Chicago. So. I don't know whether PhD programs prefer not to have their own MA students. I hope not, and I don't think they strongly disfavor that 'cause I see offers from Chicago in the reports of every discipline.
Last thing to say. I don't think it's like you will automatically get accepted by MAPSS just because you got rejected by their PhD program, although my rejection letter came with MAPSS admission. Think about it. It's a program consisting of around 180 people from Psychology, Sociology, Anthro, Poli-Sci and History applicants. Take Soc for example, there were about 40 soc people in my cohort. Do you think there are only 40 rejected soc PhD applicants every year? (or say if there are 300 applicants every year and about 270 got rejected. That means 230 people turn down MAPSS offers. Humm...) But I'm convinced that with a decent stats you can get in.
Anyways, hope the info helps.