Perfect you answered both of your own concerns, add a new stat like concentration and put it on HQ'd gear/tools to help your materia %'s. Also you said it yourself

"thats only an animation we can assume that your tool is only prepping the item to receive the materia since they already said that you use the goggy tool to attach."

Excellent! you can improve your stats so that the item your prepping is in a better condition to receive the materia.