As a Vet, I know for a fact most people deal with multiple Chains of Command.
For example... you laid out NCOIC (E8) -> Successive Unit COs (O3 -> O5 -> O6 etc.)
But if you're maintenance, there is simultaneously also Maintenance NCOIC (E8) -> Maintenance Officer (CWO), and successive Maintenance Officers at higher unit levels (O4 -> 05 etc.)
If you're on the operations side, there is a simultaneous Duty Officer at the Battalion or Squadron level (O4) who will intercede on the CO's behalf and handle matters in a more hands-on approach. Often accompanied by his own hand-picked SNCO.
It's not always clear what falls to which chain either. Most decisions, regardless of context, in my first unit were handled as a committee by "The Four Tops" as we called them. Two E8s, a CWO4 and O3.
For about 3 months, the O3 would only come to work in the afternoons to rubber stamp paperwork; otherwise taking phone calls from the golf course. At times the two E8s would take turns on who would show up for the day and either of them would put their John Hancock to the paperwork. This might seem irresponsible, but it was during this period that the unit was most efficient, contributed significantly to the larger unit earning a NUC, and after 9/11 earned the first opportunity for our type of unit to deploy in Operations since Vietnam -- on the basis of that efficiency, and earned a MUC for that deployment.
In other instances I've encountered on the Operations side, the NCOIC and CO are practically cut out of the chain by other Officers who are more hands-on. In an Operations environment with an Officer-heavy duty roster (previous situation had 70 enlisted to 1 CWO and 1 CO... and this one had 50 Enlisted to 25 Officers), there's often no rank considerations at all. Orders come down the pipeline and could be disseminated by any number of Officers; often leading to situations of conflicting orders from people far above your pay grade. You work for different Officers every week, and while your evaluation paperwork may be filled out by 1 SNCO every time -- it'll be heavily influenced by the impressions fed to him by those Officers b/c he's not present to know what did or didn't happen himself.
And then even if we cut those out, all the extracurricular stuff have Chains of their own. There's another Chain for the Base itself; independent of your unit's command structure. There's another Chain in the Barracks. And another for PT. And another for Training. And another for COMSEC. etc. etc. etc.
Even at the top end, it's often muddled. You've got a General for the MEF containing a Wing and a Division, and his direct boss is theoretically MARFORCOM or MARFORPAC. However, if you deploy you'll generally find yourself really under a designated Theater Commander; likely via a Liaison from your Service. While simultaneously being held responsible to FORCOM or FORPAC dependent on your unit's home location. Then there's often positions for forces within a given country; which includes only part of a MEF and has no direct command over the MEF -- but to which those portions of the MEF do answer to.
TL;DR The military is far from being a straight up-and-down Hierarchical structure. Unless you're a non-rate answering to an NCO directly above you; there's another boss in every direction. And commonly these bosses hold power over people of lower rank due to the Billet. ie: Base CO being a Colonel holding sway over a Brig. Gen., whose unit resides on that base, on certain matters.
When we deployed, the Chair Force and Army had a power struggle over the base. On paper it was an Army base, with the Base Commander starting off as a Colonel. However, the importance and relevance of the base was undoubtedly tied to the Air Force. The Army merely had HQ sections for 10th Mountain and 82nd Airborne there. The actual combat elements were elsewhere. Whereas the Air Force operated out of this base providing CAS and AMC to various combat elements throughout the theater (not just the 10th or 82nd.)
Fed up with some of the asinine Army bs, the Air Force brought in a Star who promptly told the Army to shove it. The Army then brought in their own Brig. Gen.; and made even more asinine rules such as mandating that kevlars and flak jacket must be worn for "safety" while operating a Gator and limiting base-wide speed limit to 5mph
Best part is, our CWO (with only the backing of a Captain on the bring of derangement) told all of them to take a hike. And when General Pace (then Vice Chairmain JCOS) arrived, and they apparently complained, he had our backs and the CWO3 became a CWO4 within the month.
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