That the heroes are only "about" to retire doesn't mean they would have been spending their last active months or years in field assignments. For all we know, the ship has seen constant and demanding service, but under a variety of commanders, with Kirk being sent only when there was a special need to provocatively show off Starfleet's greatest hero.
Various offhand remarks suggesting continuity need not be taken quite so literally. "The first Enterprise
without Kirk in command" is a valid statement (by newspaper tagline standards anyway), without having to mean that nobody else but Kirk ever commanded starships named Enterprise
. "Been starship CMO for 27 years" doesn't mean doing 27 times 365 times 24 hours of that work, only that McCoy first became a starship CMO 27 years ago. And so forth.
There's definitely room for both the interpretations on the nature of the E-A, then. If she's kept running even when Kirk is off womanizing and Spock talks peace with Klingons, then she's unlikely to be a pariah ship. But it might still be a 23rd century fact that older ships are more expensive to operate, and best kept inactive until really needed.
As for the bunk beds, there's nothing about them that would run contrary to what was actually seen in TOS. Roddenberry didn't really have all that much influence over his very own show in the end: the ship doesn't have an all-officer crew, for example. Really, most of Roddenberry's supposed dictations were probably done well after the fact, contradicting his own original thinking.
Now, bunk beds for key officers
who sleep in their service uniforms
in VOY "Flashback" can be argued to be contrary to TOS. But they are also contrary to ST6:TUC (where only enlisteds had bunk beds, in which they slept in pajamas), and to common sense. Then again, that was just a dream sequence... Perhaps the most embarrassing thing a Vulcan can dream of is wearing full clothes when not appropriate?