WinnieThePooh – I think you added a critical point. There is the “owner” of the Yeshiva, and the “Rosh Yeshiva”. While the first person makes the decisions (and is the “real” Rosh Yeshiva), the second may be brought in for whatever reason, and serves at the whim of the Yeshiva’s owners.
Ner Yisroel may be (and I’m not that familiar with the situation) a similar idea (and this may not be the Metzius, but hear me out). Although the “Rosh Yeshiva” is Rav Feldman, he serves at the whim of the Neuberger family, who installs their own people in positions of power within the organization.