Indeed it does. But it was also a great choice to be honest.
If they had just used the traditional job names from the outset for this new class system everyone would have been confused about "Well why is there a Red Mage, and a Dark Knight with no melee weapon" as Conj and Thaum seemed to fit those descriptions at first. If you think of the armoury system outside of traditional FF jobs none of the classes match any of the jobs from past FFs. Instead you have to mix and match atleast 2 classes in XIV to make a traditional FF Job. I have a feeling they always intended to have the Final Fantasy Job names play a part in character customization but they didnt get it finalized before they were forced to release so the system never came to pass. Instead Yoshi-P had to throw one together and hopefully its adequate to create a sense of accomplishment, force role reinforcement, and nostalgia. Even if its illusionary. All without removing the uniqueness of the Armoury System.