"Freeport" is a pretty generic name, so it's not surprising to see it used in a context unrelated to GR's city. After all, with so many worlds, there are many, many "free ports".
And from the posted intro, the EQ city is a rather distinct creature from GR's ex-pirate town. Even the maps aren't that similar, beyond the historically common "port town sprawling around central keep" model.
A couple guys who played in my Freeport campaign also play EQ online regularly. I'm in another game with them where I'm the only player who doesn't
game online. My game's been mentioned around that group, but after we clarified that it was a different Freeport, they had no problem with the name being the same. Simple: If anyone mentions Tim and Freeport in the same breath, they're not talking about EQ.