^ That's probably a fair assessment. But, as you say, canon has shown us that Starfleet did start using the term that way, so I think we're stuck with it.
Now, interestingly, I'm not sure we ever heard the term "flagship" applied to any version of the Enterprise
other than the D. It certainly was never used in TOS or even the TOS movies that I recall. When a new ship was christened the Enterprise
-A was, I believe, the point at which it seems that there began to be a special reverence attached. But I don't recall any others but the D actually being called that.
Which makes me wonder if Starfleet considered the B, or the C, or the E to be their flagship?