I don't think I'd jump to that conclusion. The data shows that the 25-75%ile spread for Step 1 score is fairly weakly correlated to entering MCAT score, suggesting that 1) if the MSTP group does indeed have a significantly higher MCAT distribution than the rest of the MD class, it is unlikely to make a significant impact on the Step 1 score, and 2) Step 1 performance is likely more closely related with individual habits/study techniques than it is with raw test taking ability, although being good at preparing for standardized tests does indeed predict that you will be good at preparing for other standardized tests.
What I've heard at my institution is that MSTP grads tend to match much higher in the more "science friendly" specialties (Path, Med, Peds, Neuro, Peds-Neuro) at significantly lower Step 1 scores than you'd expect but have to score virtually the same as the MD-only cohort to match in the super-competitive, non-science friendly specialties (Ortho, ENT, Urology, Ophtho). Although this might be, as one of my mentors (a surgeon scientist) suggested, due to the fact that there are only 3-4 institutions genuinely supportive of surgeons doing translational/bench science and they tend to be the most competitive places to match but they might also be the only places that care about your PhD. There are a few competitive specialties that are a bit more friendly towards MD/PhD grads than most of the surgical supspecialties (Derm, NSG).
There's no getting around the fact that you have to perform well on Step 1 and during your clerkships, but, as you say, MSTP grads do tend to match at very good academic residencies most of the time in the specialties and institutions with longer track records of training physician scientists. I think it's unlikely that this can be boiled down simply to just "MSTP students do better on Step 1" (which I think might actually be the reverse of the truth lol but thats just my speculation) or "The PhD is your golden ticket to a top academic hospital" (which may have been true 20 years ago but it certainly isnt today).
All in all I'd spend like 0 seconds worrying about Step 1 when choosing a program. The track record of getting their students where they want to go and training people who are graduating on time and motivated to keep going (and of course where you can see yourself thriving for 7+ years) is more important.
