I would recommend looking very closely at the environment right now at NYU before making your decision as a lot of what people mentioned regarding the NYU MSTP offers being rescinded centered around a lack of institutional funding for both the MD and MD/PhD. In an environment like that, will you be able to or have support to do additional research? Along with that, look at the institution that you are considering for MD/PhD. During my second looks, schools told me about certain donations the schools had received recently or other signs of institutional funding ie hiring faculty, involvement of high level people within the hospital system/medical school at the second looks. which demonstrated that if all things fail, the school itself cares about the md/phd program enough that it would make sure those students were supported.
Additionally, to your second point, I think it really depends on how you envision your own research direction going. The reality is that science now vs science of the past is very different. I have had interviewers and mentors discuss the difficulty of getting their foot in the door of research as MDs, but they also were able to get there. I think ultimately, you won't be closing doors, but it's a difference of how you get there and the time you would have put into getting a PhD will be allocated and spent in other parts of your career to become an MD-only physician-scientist.