seems like it would be labor intensive. why not train your crew to use cups and portion the right way, train your managers to be vigilant about it. when I was at Pizza hut the cooks either portioned cheese and toppings right or they got fired.
I have used bags to portion. Huge pain and it is hard to tell them apart and in a rush they WILL get mixed up! I stopped bagging and went to a cup on the make line that we used. In the new store we will have a cup on the line as well!
Trying to ‘economize’ using a disposable bag seems counter-intuitive to me. It could be done weaily enough, and the storage on make line would be simple, the the few pennies a bag would eat some of yor savings right up from each pie.