>>96729718
>Recent fluff
>It also doesn't help that Custodes like the sisters more than they like marines so according to the sister codex they side with them much more often during disputes.
I guess that would explain it. Custodes were and always will be Palace Guard and nothing more to me.

As far as I can tell SoB do not have any direct power over SM whatsoever. They are part of the Ministorum. As such they might have political power, but no actual authority.