Probably done to keep from confusing the audience, many of which wouldn't have any understanding of military procedure.
And since Starfleet claims not to be a military organization, who knows what their orders of command are.
Yeah...not to hijack the thread but if you believe that "Starfleet wasn't meant to be a military organization" crap Roddenberry spouted off after TMP, then you might as well believe all those shady looking Asian "massage" parlors just give massages.
You cannot have a show where starfleet, from the very first episode of TOS, is structured almost exactly like the United States Navy, uses countless military organizational components, terminology and many other elements and then say "This was NEVER meant to be military in nature."
Just one example: the name USS Enterprise. USS IRL stands for United States Ship and is used by the Navy as a prefix on all its commissioned warships. I know in ST is stands for United Star Ship, but the show could have used other prefixes like United Federation Ship, Federation Exploration Ship, Federation Starfleet Craft.......and many others that wouldn't have been USS and a direct link to the Navy, which last I checked is very much a military organization.
As for the name. If Roddenberry was so steadfast that starfleet's mission was exploration and discovery and not military in nature he could have called the ship many names: Explorer, Voyager, Discovery, Peacekeeper, Reliant, Freedom, etc. that denoted a peaceful nature. Hell he could have called it the Shamrock......None of these names had any well known to the US Navy.
As fate would have it he chose the name "Enterprise" why? Well in the 25 years preceding the start of ST there had been two very famous vessels named Enterprise. Both were aircraft carriers and were in the US Navy.
The first carrier Enterprise CV-6 was commissioned a few years before WWII began. Should have been at Pearl Harbor on Dec 7th, but got delayed by a storm and of the 6 aircraft carriers that fought in the Pacific in the first year of the war only she and the USS Saratoga were still afloat at the end of 1942. Enterprise however fought practically non stop in 1942 and several times was the only operational carrier standing between the Japanese Navy and some major victory. While Saratoga had an unfortunate habit of being torpedoed by submarines just before major battles (happened twice) which caused her to miss several engagements before joining the fray in late 1942.
Enterprise then went on to have the most decorated career of any WARSHIP in US Navy history. And by all rights should have been preserved as a memorial after WWII and her scrapping is a national disgrace. Like if they built a strip mall on Gettysburg.
The second carrier Enterprise CVN-65 was commissioned in 1961 and at the time of ST's premier was the largest, longest and most powerful WARSHIP in the world. She was also the first nuclear powered carrier......nuclear isn't exactly a word that brings to mind peaceful intentions. Oh and she was involved heavily in providing air support in the Vietnam WAR during much of the show's run.
So Roddenberry named the starship Enterprise after the most decorated WARSHIP in US history which fought in the largest war ever and was only 20 years in the past when ST premiered. As well as the most powerful WARSHIP afloat at the time, which was also actively involved in combat operations when ST premiered.
That is but one small example but really you cannot be more obvious about making a strong military connection to the show by calling the main setting the USS Enterprise. He literally could not have picked a name that had a more militaristic connection to it because of the prefix being a real life Navy one and the fame of the name "Enterprise" in US Navy history.
This "Starfleet was never meant to be a military organization" is a bunch of crap Roddenberry started pushing hard, and other defenders of him continued, after he got kicked out of the loop after TMP and and he wanted to make it look like Paramount with Meyer and Bennett had ruined his "vision" of Star Trek.
Yeah starfleet had a NASA like element to it of exploration no doubt. But you know what? The US Military often participates in exploration and scientific missions, sometimes it's to help create stronger weapons...but other times there is no combat element involved in their participation. But noone would call the Navy, Army and Air Force anything other than military organizations first and foremost.
All Meyer and Bennett did was make the military element more prominent and consistent with things like matching uniforms and hallways that resembled those found on naval warships. They didn't "ruin" anything of Gene's "vision"...because this non-military utopian society "vision" Roddenberry was so fond of was just his anger at Paramount and trying to garner sympathy from ST fans because they were "destroying" everything he worked so hard to create.......Yet didn't really seem to start heavily talking about until 1979 when he was kicked out of the decision making loop.
I could write a 300 page book on the ways starfleet is most certainly a military organization above all based on it's design from the very start. This "It's a primary peaceful, scientific, discovery" organization is a bunch of utter nonsense and wasn't a man's "vision" but his way at trying to get back at those who he felt screwed over by.
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