In order to attach materia to Rare/Ex I believe they only have a few ways to do it:

Options A
If Rare/Ex get materia they will become very powerful compared to Crafting items. The crafting items will have to get buffed to compensate for this to be equivalent to Rare/Ex. I'm afraid if this happens, why bother raiding when you can make the most powerful items from crafting.

Option B
The crafting items aren't buffed. Then dungeon items plus materia become the strongest items and make most of crafting useless (with exception of adding the materia).

Option C
Rare/Ex get maybe 2 materia and Crafting items get all 5. They converge to approximately the same item power. Rare/Ex + 2 materia requires raiding a dungeon and a little bit of luck for 2 materia but crafting plus 5 materia require a lot of luck but no raiding.

What do you think? How can they allow Rare/Ex plus materia in your mind?