It's more about scheduling and flexibility (potentially) during 4th year, not about clinical knowledge or getting honors during 3rd year. At our institution there is no elective time until 4th year, which starts in May. That normally gives you ~4.5 months for subIs and electives for letters and career exploration before ERAS opens. Any 3rd year rotations missed because of a late return are made up at the beginning of 4th year. Potentially losing even 2 of those months as a result makes career exploration, letter hunting, and general scheduling that much more difficult and less flexible.
Choosing a split 3rd year can really only help you; there aren't that many major disadvantages. Our program has been offering this option for the last 7 years and it's been received very well.
I am not sure what you are saying here, and there seems to be a lot of confusion in this thread. What it boils down to is that any time spent doing clerkships prior to PhD will mean more time tacked on to the end of PhD, so you end up going back late to 3rd year. I personally have never witnessed somebody do clerkships prior to the PhD and then start MS3 year at the exact same time as MD-only MS3s. There is something psychological about "having already done clerkships" that makes people drag out their PhD, so they SAVE NO TIME.
So then the issue boils down to just a few things:
1) will your experience in one or two MS3 clerkships help during your PhD? I think this one is very easy. The answer is no.
2) will starting one or two MS3 clerkships at the same time as your MD-only classmates help you at the beginning of your mini-MS3? The answer is no, because you are on an equal footing, just coming off of MS2.
3) will starting the remainder of your MS3 clerkships late, with a 3-5 year hiatus from any prior clinical experience (save half day shadowing and the like done during the PhD), help you or hurt you during the bulk of your MS3 year? This one is also easy--it hurts a lot. I hear a lot of MSTPs complain that "it's so hard to do well in MS3 because we're so far removed from MS1-2 and clinical knowledge.
Ladies and gentlemen, the solution is to start MS3 when everybody else does, and then work your ass off, reading twice as much every night when you're dead-tired, to catch up on your knowledge. If you do this, coupled with your - let's face it, superiority relative to MD-only students at studying and retaining knowledge - and your maturity, owing to age, which the members of your clinical team will appreciate, you can absolutley excel in MS3 as an MSTP. HOWEVER, if you come back 1-2 clerkships behind, it is almost impossible to pull this off. It took me two of my six clerkships before I could really shine. Had I been two clerkships behind, I would have been nearly done with MS3 before I started to pull ahead of my classmates and start raking in the Honors. As it stands now, I'm all set for AOA.
Thus, I would very strongly caution against doing any clerkships prior to starting your PhD. I would also caution very strongly against starting MS3 even one clerkship late. For some people, particularly those without the motivation to bust their ass as an MS3, it may even make sense to extend their PhD an additional 10 months so as to start MS3 on time with other students. Of course, this all presumes that you want to get Honors, etc. in MS3. If you are planning on Peds, Path, or post-doc, then it's moot.