I find this one pretty clear. Yes the Aetheryte is not directly next to the pub but when ever I need to visit the pub, which is quite often, I would use that Aetheryte and not any others even if it's not named that way. After the 3rd day, I've already gotten used to all the Aethrytes in Ishgard and none of this is any problem.

Plus the pub is like less than 5 seconds walk away from the Aetheryte so it is close to it. When I go to use this Aetheryte for things other than the pub, I think "Where is this place near? Oh the pub, so I'll use the pub Aetheryte."