You're impression of the programs and their goals is correct, but the programs tend to feel (it seems to me) that anyone not open to or perhaps preferring the idea of getting a PhD isn't serious enough about considering research in their career to be worth giving a spot to. Maybe the perception is that MD-only applicants just want research experience to pad their apps, who knows. I think it's a bit of a broken system, since many students who don't desire a primarily-research career or can't make that call yet can greatly benefit from the experience and still go on to do research.
If you select MD only on the relevant application section you may face difficulty gaining acceptance at some programs, but if you would never consider a PhD as well then the other option is lying (which is bad). That said, a lot of people just lie and put MD/PhD to get accepted to the summer programs (this according to people I've talked to both on SDN and at the program I attended).
It a weird situation. Personally I was interested in seeing what MD/PhD would be like, so I put that and worked with an MD/PhD student during the program. I thought it was a great experience even though I learned that I would prefer MD only. The "rank your degree preference" question is especially hard if you don't know, so I would just go by interest in terms of what you want to learn the most about as a career path.
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