I mean, basically you're saying that there aren't a lot in the way of tangible differences between the eras that are going to directly affect the plotting of your story. The converse of that is that if you find yourself able to tell a story in the 5YM setting, chances are it's also going to work in the movie era setting. But because of what the different context does in the readers' minds, it can make the difference between "oh, another 5YM story" to "interesting", more so if they've recently overdosed on 5YM stories.
On the other hand, there were a number of novels in the '80s that were set in the movie era but didn't really do much with the setting, and that did get a little frustrating. One of the things that prodded me to develop
Ex Machina was that nobody had ever attempted to explore Spock's journey after his life-changing epiphany about emotion in TMP, or how he got from there to the serene, self-assured Spock we saw in subsequent movies. Either they ignored the question altogether or (in the case of
The Prometheus Design by Marshak & Culbreath) they overtly reversed Spock's character growth and had him re-embrace total logic with a vengeance, which didn't make a dang bit of sense.
Nor did the post-TMP novelists before me ever really make any use of the more diverse, multispecies crew TMP introduced. Diane Duane took this concept and ran with it (though without using the same alien species), but her books were implicitly set in a hypothetical second 5-year mission (or at least a prolonged tour of duty) between TOS and TMP. The novels that were explicitly set post-TMP pretty much just gave us the same overwhelmingly human crew that TOS and the later movies employed. The only author who did anything with the alien crew from TMP was Thomas Warkentin in the syndicated comic strip.
Probably the authors who made the best use of the setting in the past were Julia Ecklar, Karen Rose Cercone, and Melissa Crandall (both writing together as L. A. Graf and in Ecklar & Crandall's solo novels), who always made security chief Chekov a central character in their post-TMP books. But they still didn't do much with any other aspects of the post-TMP setting (probably because they were approaching it more as a pre-TWOK setting).
To me, there are a lot of differences between the TOS and post-TMP settings, both large and small. Spock's more mature personality, Chekov's new job, Chief DiFalco and the other bit players, the multispecies crew, the new designs and technology like the bigger shuttlebay and the tubular intermix chamber and the clothing transporters and the security helmets/armor, the dual deflector/force field system, etc. As long as you actually make use of those elements instead of glossing over them, then I think you could make a post-TMP novel feel distinct from a TOS-era novel even if the plot is one that could work in either.
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