Please don't take this wrong way and this is just my opinion, but I see some serious disadvantages to organizing an MD/PhD program that way.
1. MS4 certainly has the potential to be a total waste of time, but I think there is something to be said even for that. I have essentially 6 months of vacation. This is the last really carefree time in my life before I enter the grind for 30+ years...I guess I could go roaring into internship straight out of my clinical clerkships, but I kinda like the chance to recharge my batteries, play with my kids, etc. before all hell breaks loose and I am q4 for 9mo. Plus, not all 4th year electives are total throwaways like wilderness medicine...ICU months are great and even cush subspecialty months can be of benefit (e.g. derm). I learned more in 4 weeks in the MICU than I did in all the rest of med school. I only did 4 months in 4th year, but those were 4 quality months with no throwaways (solid primary care bread/butter outpt medicine, hard core bread/butter inpatient medicine, MICU, and neurology) and I definitely feel like I am much stronger/more competent clinically now than I was at the end of 3rd year. Although I will still wet my pants my first call night.
2. Doing IM before PhD: What if you want to do IM? Does it matter that your LORs are 5 years old? Are you able to shine on an IM sub-I and get that great LOR when your original IM clerkship was 4 years ago? I don't know about you, but I'm stupid enough where I could barely remember what my name was after 4 years of grad school, let alone the DDx for acute renal failure.
3. So then you do IM, plus one other required rotation, plus a Sub-I before applying for residency? What if you are trying to decide between anesthesia, rad onc, and radiology? Do you just have to pick one Sub-I to do and decide that is what you want to match in? What if one is early match like Urology? What if you are trying to decide between IM, Peds, ENT, Rad Onc? Are you screwed because there is no possible way to test them all out before you have to apply to residency?
4. Step 2 CK, CS, interviews in the middle of clerkships like surgery, ob-gyn, etc. not to mention studying for SHELFS??? What if you are going for derm or rad onc and have to interview at 40+ rad-onc and prelim programs? When is there time for this? Do you hold your bowels from Nov to Feb to save precious time? More power to you if you can pull this off, but sounds crazy to me.
5. Just curious - is your 6y program MD/PhD or MSTP?
I totally agree with you that residents could be totally competent (even outstanding) with only one year of clinical training under their belt, and that there is definitely something to be said for a 6y MD/PhD track especially if you planning to be primarily a basic scientist with minimal clinical time. But logistically and from a stress/lifestyle perspective it sounds brutal. And then you go straight into a hell year of internship? Y'all are tougher than me.