An accident of the English language; some people would insist on "chairperson" there, and some older people might still insist on "chairman" but that's becoming less and less acceptable over time. As an even better example, there's "fluke":

1. A fish, and a flatworm.

2. The end parts of an anchor.

3. The fins on a whale's tail.

4. A stroke of luck.

The meanings are etymologically distinct (for the most part) and it's only chance they ended up wit the same spelling and pronunciation.

If that's philosophically troublesome, linguistics is not for you.

There’s a bit of leeway here, since that’s the word used in a different sense. But I would say that if you ask someone to “define what a chair is” that the word is being used in one sense only, compared to what happens when you ask someone to “define what ‘chair’ means” which is about the word.

That is, when we refer to a word like “chair” we use quotes, but without the quotes, we can say that an accounting department chair is not a chair.

Alternatively, we could analyze “accounting department chair” as a use of metonymy.

limited namespace conflict? Same word, different abstract concept than the chair under question

I always assumed it came by naming the person who sat in the special seat after the seat itself.

This has a name! It’s called “metonymy.” It’s incredibly common in casual speech and poses unique challenges for natural language processing. https://en.wikipedia.org/wiki/Metonymy

that might be the case but the person himself is not an object to be sat upon (though this may be true metaphorically... hopefully not literally).

“The person that sits in the chair generally used by the head of the accounting department” :)