This apparently resulted from the reworking of a game called Penguin, in which you stack coloured penguins into a pyramid, into a game called Game of Thrones: Westeros Intrigue, in which you play cards representing characters from one of four of the noble houses from that fictional setting into a pyramid arrangement. Mechanically, these are the same game. Although the construction and appearance of these games are markedly different, the rules governing what you do with them are identical.
As such, BGG gave them both the same listing. If you went to the page on BGG for GoT:WI, you'd see photos of both games jumbled together in the Images section, and a listing for 'Alternate Names' that included Penguin. But if you did a search for 'Antarctic Theme,' you'd get GoT:WI in the results, due to it being linked with Penguin.
Understandably, this caused some confusion. Not to mention that fans of George R. R. Martin's books were not pleased about the association with a silly, fluffy kids game of stacking penguins (despite the fact that they're doing the same thing with non-silly, non-fluffy characters). So BGG created and implemented their 'reimplements' system. Now, Penguin and GoT:WI are listed as separate games, but are linked to each other.
This is the case for a number of other games as well. Some are games that have been completely rethemed, as in the case of Risk Express, which was reworked into Age of War. Other examples include games that went out of print, and were brought back into print later with a new theme, as was the case with Clans and Fae. There are even some instances of a game being rethemed whilst it was still in print, by the same company. This is what happened with Century: Spice Road and Century: Golem Edition.
But as the forum entry on BGG by one of the admins describing the creation of the reimplementation system points out, retheming a game is not dissimilar from translating it into a new language. Once you know the vocabulary being used to describe the mechanics, you're still performing the same actions, following the same rules, and striving for the same win conditions.
Case in point: in Clans, you're working to bring Pleistocene settlers together to form villages, taking care to settle in favoured terrain and avoid unfavoured terrain. In Fae, you're working to bring druids together to form rituals, taking care to perform these rituals in blessed terrain and avoid cursed terrain. Mechanically, you're doing the exact same thing. The only difference is the appearance and construction of the pieces and the words you use to talk about the game.
So are they the same game?
I don't know. I can't answer that question.
For some people, the answer is yes. I certainly treated the two games as one when logging plays for the 10×10 Challenge. But for me, theme isn't always that important. If it were, I would likely have enjoyed The Princess Bride: Storming the Castle much more than I actually did.
Other players place a greater emphasis on theme, however. In the forum discussions concerning the reprint of Clans as Fae, for example, many people said they didn't like the new theme, and would only grudgingly purchase the new version if it meant that new players were more willing to give it a try than they had been with the original.
So I suppose the ultimate answer is: it depends on your perspective. Some people will draw the line between two games differently than others. But whatever your thoughts on the matter are, I hope that this has given you something to think about. And whatever you think about it, I hope you always