I am at one of the above programs, and I think we greatly benefit from having the first clinical year done before the PhD because
(1) As mentioned, it makes your research more relevant to your future clinical work. I came in thinking one field, but after experiencing it clinically hated it and went in a completely different direction. Others have as well, while many students have their initial interests confirmed.
(2) It is not just the 4 years away-- and the forgetting of information-- that would make doing the clinical year after the PhD hard. It is an emotionally challenging year, and being able to go through it/commiserating with my friends who entered medical school with me is probably what kept me the most sane. I can't imagine going through that year with a cohort that I barely met.
Regarding logistics for MS4, the biggest challenge is scheduling a defense date and return to the medical school, though this is now so streamlined that it is not an issue. Generally students come back in time for 2 "warm-up" rotations (usually an outpatient rotation followed by an inpatient consult service) before doing their Sub-I. If you plan poorly, you may end up returning and having to do your Sub-I right away, which is not ideal and discouraged by the program. I would say 90+% of students make the above "ideal" schedule work.