Specs: quill stem, carbon fork, stem nut bolt comes out all the way, but stem won't come out.

I tried putting lube through the hole where the bolt is and through the other end, upside down. I've read that you're supposed to screw the stem bolt in until there are a couple rotations left, gently hammer the bolt to loosen to wedge. My question is, wouldn't that make the wedge further stuck? I turned the bike upside down and tapped on the fork and headtube gently.

Any other suggestions?

Only occasionally, on steerer tubes that have smaller inside diameters down near the crown. Not necessarily on steerer tubes that have a constant ID.

Get that bolt back in, put scrap wood over it and whack with hammer.
If you have a drift punch or similar, you can try hitting the bottom with that while bike is flipped over.

And soak it with some solvents and pray for the best.

Yep, the advice you already got is the best: screw the bolt in a few turns so the head is poking out, then tap sharply with a metal hammer. If you can get someone to hold the fork for you, place a small socket atop the bolt head to avoid damaging it with the hammer. Works like a charm, or at least has on every stuck quill I've ever had to deal with.

So if I'm understanding this correctly, the bolt should be in its normal location, at the top. It should be screwed a bit loosely. Then I hit the bolt with a hammer from the top.

This didn't work for me, so should I try ammonia or liquid wrench/similar?

These are like $1.99 at Harbor Freight.

A very useful tool to have around the bike workshop.

Update: either the wedge was loosened or the threads in the wedge were destroyed by the hammer. I think the wedge is inside the steerer now, BUT the stem is still stuck. I think it's fused with the headset, but is there a way to remove the headset while the stem is still on?

Nevermind. It all worked. Wedge was loose and I just had to pry the stem off. Thanks everyone.