How can someone think that two different buildings - the Palace and Governor's Residence - could be the same building?
I don't think he thought they were the same building. I think he assumed the Palace and Governor's Residence would be interchangeable for the purpose of fulfilling the requirements for the dockyard. At least that's my interpretation based on his statement:
I assumed Palace would be interchangeable with the GR in this
As to the impending follow-up questions of "why would you make an assumption like that? The description doesn't say Palace, it says Governor's Residence, and it means exactly what it says and not one word extra, I can't see any possible reason why anyone would assume that it means more than exactly what it says", well I can't answer for him, but I can at least give my own opinion.
I can see why one would assume that the description saying "Governor's Residence" was supposed to mean "Governor's Residence or Palace" and that the person who wrote the description just forgot to include Palace. That seems like a reasonable assumption to me. Mainly because, there is seemingly no obvious reason to exclude the Palace, whereas making a typo is a fairly easy to mistake to imagine (I recall we used to have a whole category for "text issues" where random phrases and interfaces would be untranslated from German). So then it's just a question of "is it more likely that the game developers intentionally excluded the Palace for no apparent reason, or that they just forgot to include it in the description?" The second seems much more likely, so I can see why someone would assume it was so.
I also think it's quite normal that people consider the Palace and Governor's Residence as being interchangeable. They are for most intents and purposes the same building. They are unlocked at the same time, perform the same function in the town, they have identical building cost and building time. They also open up the same "Towns in your empire" interface when clicked on; the only difference is the Palace has the extra button for changing form of government.


And, what's this? That's interesting, it says "Palace" for the whole column, but we know only one of them is a Palace and the rest are GRs.

That's funny. It seems even Gameforge considers them to be basically interchangeable. Actually it's an example of this exact assumption in action. The literal text just says "Palace" and nothing else, but it actually means "Palace or Governor's Residence" in reality. So, I can definitely see why some people would think that the Dockyard requirement includes Palaces even though the description doesn't mention it specifically. I don't think it's strange at all.
Personally I think the Palace should also count, I really don't see any reason why it should be excluded. But if not, then I think the description should be changed to add "A Palace does not fulfill this requirement at the end." to remove all possibility of confusion.