The same way any capable writer handles exposition. If you know that a word is being used in an unconventional way, then you know that someone in your audience will catch it, so you'd bloody well better include something in-story to explain why it's being used differently. There are plenty of ways to incorporate such exposition into a story organically. So if it isn't there, that implies that the creators didn't realize it was being used unconventionally.
Besides, we've had a half-century of Star Trek in which characters have consistently used the English language in the same way that contemporary audiences used it (profanity aside). If they had made a deliberate choice to establish that one word had changed its meaning over the centuries, then presumably they would've done so with other words as well. But they didn't. There were other SF shows that did make a conscious effort to establish a futuristic or alien vocabulary for their characters -- e.g. the future soldier's slang in Harlan Ellison's Outer Limits episode "Soldier," or the Colonial vocabulary in the original Battlestar Galactica -- but ST has always used ordinary 20th/21st-century English aside from added terms for new technologies. So it just doesn't wash to claim that they'd choose to "evolve the meaning" of exactly one word and no others. Especially when the meaning they used for "flagship" isn't futuristic at all, just present-day civilian vernacular.
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