And even if the j.g. rank was only rarely used in the 23rd Century of the Prime Universe, it's possible that this may have changed in the Kelvin Universe. (Yes, I may well be fudging things there, too--but I'll take anything that makes Kirk's promotion at the end of ST09 look less implausible, even if we're only moving from a four-grade to a three-grade promotion.)
Well, Tormolen wore the stripes of a lieutenant j.g. (presumably), but TOS costuming was often inconsistent in its portrayals of rank (for instance Spock wearing full commander's stripes but being called a lieutenant commander in dialogue, or various lieutenants having completely bare sleeves). That was such an early episode that a lot of things hadn't yet been locked down, and no rank for Tormolen was stated in dialogue. So I'm not prepared to take the existence of the j.g. rank in the 2260s as absolutely confirmed when it might've simply been a production inconsistency. A single data point without corroboration should never be taken as solid proof of anything, and Tormolen is the only character in any 23rd-century production even implied to have that rank.
^ If they bothered to create Tormolen's rank stripes at all, then they must have intended the rank to exist.
No, the studio seamstress had made a variety of velour tops, with differing rank on each for visual variety - and someone grabbed one that fitted to dress the actor for the scene. It wasn't till ST:TMP that they even grappled with the fact that Crewman and Ensign rank both meant "sleeves with no braid" in TOS.
You might as well say that they intended Spock's species to be Vulcanians or the Enterprise to be operated by UESPA or the ship to be powered by lithium crystals. "The Naked Time" was only the seventh episode produced. A lot of stuff was still in flux that early on. Their intention wasn't to carve anything in stone, it was to try things out and see what worked, to make it up as they went along and refine their ideas along the way. For all we know, the half-stripe may have been a rejected idea for ensign rank, and they just happened to keep the costume around and grabbed it when they needed to dress Stewart Moss in a uniform. Since they never actually stated onscreen what rank it represented, it's only an assumption after the fact that it was supposed to be lieutenant junior grade.