I would discontinue using the NIX as a precaution. No need to expose your snake to the poison when he doesn't even have mites. Lots of people will treat a new addition while they have it in QT to make sure they don't introduce mites to their collection, but that is different than doing it repeatedly.
If you do ever have a case of mites and need to deal with it, some people do use NIX successfully without problems, however as far as I am aware, no scientific testing has been done to see if it is safe for reptiles or if there may be long term negative effects. Provent-a-mite (PAM) is a product that was designed and tested specifically for use on reptiles.
As far as the food question, we could help you a lot better if we either have a pic of your snake with something in it for size reference (you could even show a pic of him with the size rat you are feeding), or if you can give us an accurate weight.
A size comparison to one other BP is not enough to assume your BP has been underfed. Females get quite a bit bigger than males usually, so if the other one was female, that could be one explanation for it.