We need to recall that Security Assistance is a DOS program enabled (or constrained) by the Foreign Assistance Act (FAA) of 1961 (as amended) and the Arms Export Control Act (AECA) of 1976 (as amended). Any program funded and/or controlled by these acts is subject to DOS supervision at the very least. Most FID is funded as FMS/FMF(a bit under IMET and ESF) which are all FAA programs. While there is some counternarcotics funding not under the FAA and programs of Joint Exercises (JCETs for example) and Title 10 H/CA these are merely add ons to FID programs funded by FAA. And, these "add ons" are subject to the approval of the Amb whio is advised by his Country Team (only 2 members of which wear uniforms - most of the rest are DOS).

One might be able to make a distinction between FID - a normal program run by the Amb and his CT and SFA in the midst of a major military operation. Yet, i am not sure the distinction is real or valid. I would argue that the SFA mission in Iraq was relatively successful due, in large part, to the mind meld of GEN petraeus and Amb Crocker. So, who had the lead C or P or P or C? Yes! But that is what makes the situation so unusual and it was made to work by the 2 guys on the ground. There is no standard "command relationship" that can dictate such a structure and a reluctance on the part of all presidents in my lifetime to say who is in charge of such a situation.

Your point that constrained resources makes people use what they have more effectively (and efficiently) is wise.