The next update will justify the reason for a universal repair item(s). It might be safe to say that materia will eat up slots when an armor is changed into a materia, and it may also be safe to say that the gear will need to be at 100% in order to turn into materia.
With these two simple ideas in mind it brings a lot less stress to creating the materia system and the overall value of repairing gear will be based on the materia it can create. In a sense crafters will have two new markets opened to them once materia is introduced.
The first market will be the demand for 100% repair to turn a piece of gear into materia, then the second demand will be infusing said materia into another piece of armor. One thing I wonder though is how will materia work? Will it work like repairs where a person puts it in their bazaar along with the gear they want infused and the crafter simply agrees to do it and if they succeed the materia is infused into the gear and they obtain the reward. I think that would be the best way to do it unless they can implement a craft system where you don't have to trade gear to the crafter and hope they give it back to you lol.
When it comes down to materia they could make the cost of each attempt be shards/crystals/clusters based on the materia being infused in the armor so overall I don't see much concern for crafters and believe that with the upcoming update they will have a more defined as a class in terms of bringing support to their fellow adventurers.