Few points. Just because it is hard to get doesn't mean it has to be the best. There are trophy pieces. And, although this isn't FFXI, SE has a precedent for having impossibily hard to obtain items with little or less than best practical value (some relics and mystics and even mob drops like Raphael's Rod or PW drops).

Also, if those same epic monsters drop legendary pieces (their horn, skin, what-have-you) and a master artisan puts those pieces together to make an epic weapon (morningstar from castlevania anyone?) that should/could be best in slot. I don't think it has to be one way or other but can be a mix.

All that said, it will be weird if you can buy an npc sold sword and add 5-materia to it and make it better than the sword that drops from 5th chest Batrael. That is why I am sort of pro-socket idea like WoW and other MMOs, because the items can be limited in their potential (i.e., a npc bought sword would only have 1 socket whereas Batrael sword 3 possible sockets). Will be interesting to see how it all works out.