I think the same effect can be had without adding a new system that may turn out to be complex to implement.

Facilities (e.g. Forges, Gemmaries) give bonuses their respective crafts. Right now any class (i.e. Pugilists, Conjurers) can pay for access to ANY facility and get the bonus, even if it's useless to them. Maybe some minor restriction might be in order so that a smaller subset of players have access to these facilities. Sidequests, Class Quests, Guild Quests, or Minimum Level, are all possibilities for granting or restricting facility access ... in addition to the gil fee.

In addition, the Grand Companies may have facilities of their own (they are supposed to be grand and all) which may be superior to the ones available at guilds. Of course, only company members of a certain rank or higher may be permitted to use these incredible facilities to fashion truly epic +4, +5, and +6 HQ equipment.

Just an idea.