Wowzers! I have to agree w/ Neuronix and Maebea. Though what you posted has some truths in it, it is highly misleading.
This is not necessarily true. Some schools simply waive tuition rather than charge you for it and then credit you through a scholarship fund.
While it is true that many NIH-funded MSTPs (a redundant statement really, all MSTPs are, by definition, federally funded) fund their programs through a mix of private, public, and NIH funds, the payback policy is the the same.
If a program violates NIH policy by forcing a MSTP drop-out to pay back their stipend, then they will lose accredidation and funding, simple as that.
The rule is there for a very good reason. An MSTP is a long, difficult, drawn-out process and one never knows what fate will have in store for them over the next 7-9 years. People should NEVER be penalized for dropping out, IMO.
Non-MSTPs face a different reality. Their programs are funded 100% by private/state funds. They are putting up their own money and do not have an obligation to the NIH, so you must pay them back. Since you go in with this understanding, they are not misleading applicants.
The NIH-funded MSTP is a fairly new development. I think only 17 schools had NIH-funded spots in 2000, and some current schools have a mix between NIH and privately-funded spots.
As Maebea said, NIH-funded MSTPs have been around for more than four decades.
Once you actually get admitted to a program that has the money guaranteed for you in some way, the distinction between an NIH-funded MSTP and a "non-MSTP MD/PhD" exists only in myth.
This is a loaded statement. No doubt that someone who undergoes the rigors of an MD/PhD program and completes it is most likely highly qualifed to enter academic medicine.
But MD/PhD programs who have MSTP status have it for a reason. And it's not b/c of "prestige." Schools who apply to for MSTP status have to show many things (and show them again when it comes time for renewal) including:
1. High retention of students
2. Show that grads actually GO into academic medicine
3. Have a good breadth and depth of graduate education
4. Have a strong formalized MSTP combining grad and med school -- integrating the two well w/ coursework and research seminars
5. Strong minority recruitment
6. Strong, well-funded faculty
7. A long and well-established MD/PhD program
etc, etc, etc.
If you do not get into an MSTP, then going to a full-funded MD/PhD program is a good option. However, barring personal preference I would always choose an MSTP over a non-MSTP.