One ought to consider professional goals prior to applying to non-academic-run fellowships.
If one seeks to get paid reading biopsies in a lab after fellowship, then the non-academic fellowship is not a bad choice, as it would serve as an apprenticeship, where one would have quite a bit of autonomy over cases, see high volume, and basically hone their skills for their chosen trade.
If one would like to venture into academic medicine for a few years prior to jumping to a private practice supergroup, then perhaps it would be better to look for an academic-run fellowship, which would involve academic exercises such as tumor boards, med student/resident teaching, grand rounds, writing papers, presenting at local, regional conferences, etc.- all of which would make for a candidate better regarded to be able to engage academic practice.