To me, Scouts probably operate in a meritorcracy much as described, but when they're absorbed into the navy or marines for support or for added / augmented firepower purposes, then they have to operate with the guys who are regimented by rank.
I've never seen this addressed in any in depth manner by any official publication, nor read any article covering it.
Based upon personal opinion that when the Navy has to absorb parts of the Scout service (e.g. during a time of war), the Naval office gives each scout a rank based upon years of service. Or something similar and easy to implement without having to go through an in depth personnel review for each scout. So when the Scouts on, for example, the Naval run deep spy mission re-arrange their chain of command against the Navy supplied ranks, well confusion reigns.
I think the Marines wouldn't care. To them the Scouts are the flyboys, and crazy to boot. So either the Scouts are in charge (i.e. during normal ship operation) or the Marines are (i.e. during combat).