If you usually get 100% but sometimes it's only 94%, you're probably getting fewer Good procs on your Touch steps than usual. That's RNG you can't control.

You could play around in Teamcraft to figure out how much more Control would be needed to ensure the 100% with whatever rotation you're using but you should still usually get a HQ item even at 94%.

Spending a couple of million gil probably isn't worth it if its only going to prevent 1 or 2 NQ items in the long run. You could always use an extra HQ material if you're concerned but NQ items will also sell on the MB if for less (a lot of players only worry about meeting an ilvl requirement and don't care that the stats will be less).