I think in terms of MD programs in general, either one will work. More importantly which one do you enjoy more? Thats the most important thing about research, if you don't like it, then its not gonna be very rewarding to you as a person. Life is too short and med school is too long to lose time doing research that makes you mad..haha 😛
In terms of MSTPs, it may just depend on the background of who is looking at your application. The personnel that handle the MSTP here consist of MD/PhDs, and PhDs. Some of the PhDs do a lot of bench research so might "frown" upon clinical research. While MDs and MD/PhDs might not. I'm currently a PhD student working on clinical research for my thesis. I've been advised to pick members of my committee who have clinical backgrounds since the bench research people might "fail" me because they don't think its adequate for a PhD degree. Therefore you might run into someone like that if you are applying to an MSTP.
Personally I think that is kinda biased, but that is life. 🙄 Do what makes you happy. The good news is not a lot of people out there enjoy research, and research tends to make $$ for med schools. So regardless of what kind of research you do, you are doing something good. Of course thats just one variable out of many that determines who gets into med school...haha. 😉