Literally, no. They are not dungeons, but spiritually they carry the "dark n' dangerous" concept. They were specific areas where coffers appeared and you could not ride a chocobo into them. Throughout FF games, dungeons have always been anti-chocobo.
However I see no problem with having a mix of both. Why not have instances and open dungeon content? It doesn't specifically have to copy FFXI's dungeon system, I just used FFXI as an example in comparison, since both games are FF games and they're both MMOs.
