Sorry if I gave the impression that this will kill an application--that's definitely not what I meant. But I do think that adcoms are at least subconsciously swayed by something like this. For example, I have a friend who's a chem and math major, has done a ton of research in inorganic chem, and really wants to do his PhD in inorganic chem (via an MD/PhD program). Obviously, he's telling programs that that is his area of interest, and his application will be very coherent. If he instead told them that he wanted to do his PhD in neuroscience, when he has taken no neuroscience courses and very few biology courses, you have to think that an app reader would at least be subconsciously swayed that that's an incoherent plan - and by extension perhaps a bad idea - and that could at least slightly diminish his chances. The same would be true if I wrote that I wanted to do my PhD in inorganic chem--with only a few chem courses and no research in chem, there would be a disconnect there that would have to be at least a slight turn off to the adcom.
Of course you're right that people switch fields often, and that nobody should be expected to have done undergrad research in their PhD field. But when you're applying to MD/PhD programs against the cream of the crop, many people will have very coherent plans (e.g., a biochem major, done 3 years of biochem research, wants to be a biochemist) and it's best to have a coherent plan as well. As I said before, it doesn't matter what you actually end up doing, you just have to sell yourself and your plan. Once you're in, you can do just fine doing a PhD in any field.
But again, I don't think that this is a very important part of application at all, but every little bit helps.
FYI, my source is my PI who is on the Duke MSTP adcom, and a number of adcom members at another MSTP with which I am familiar.
