Honestly, that doesn't bother me that much. After all, TOS was made at a time when anthologies were considered the highest form of dramatic television, and so -- like many other ongoing series at the time -- TOS was designed to be essentially an anthology with continuing characters. Its strange-new-worlds format was deliberately selected to allow throwing the characters into a different kind of story every week. A tense submarine-warfare drama, a comedy-fantasy with Alice and the White Rabbit, a gangster story, a Roman epic, a Nazi story, you name it. So there was never meant to be a single, narrow definition of what "a Star Trek story" felt like. The format was intentionally created to accommodate a great diversity of genres and subject matters. Shadow Lord is Star Trek as a Meiji-era samurai epic, and that's just the sort of thing they might've done on TOS if it had been pitched to them, although their version would probably have been a lot more stereotype-laden (and would've gotten the Prime Directive right).
Also the Typhon Expanse being a settled, routinely patrolled border territory of the 23rd-century Federation, when in the episode it was uncharted territory in the 24th century.
