Yeah, I don't think that ANYTHING that crafters already over-provide should feed into the HQ rates of any new item. Let's be honest. The crafters are the problem here. Too many products. Too little to do with them.
Thus, I don't want to see any crafters blowing +3 weapons on the best materia outcomes. I'd be okay with the only meaningful $$$$$$$$$$$$ that crafters see from this system for their services is a tip for their time. The resulting gear is not going to be sellable anyway.
If they refuse to craft your materia into a weapon, I know I will do it for nothing. Your mats. You bought that weapon from me. That was my benefit.
Crafters are going to rage at that statement, but really they're already benefitting from materia even if they never synth materia synths. People buy those weapons armor and tools to destroy. They get business. They already get their reward.
You can't have crafters double dipping this system by both enjoying people buying their NQ +1 and +2 crap AND taking heavy profits from inlaying materia into things.
One or the other.