Okay...funny. HOW? Without also affecting production of the main items of the factories.
If you still want the factories output to be completely unaffected, you could make an event that counted up the number of factories, and then gave the player a fixed number of supplies and PP. A small trouble with the supplies though. They are always dealt to a hex, and the nearest HQ gets them (if there is a tie, they go to the one highest in the echelon), so, it would be guesswork, to sometimes hit the right HQ, or require some fancy coding where you gradually go up the ladder of the command structure.. and hope the player hasn't made more than one top HQ. PPs are easier to deal, since they don't require a HQ to be anywhere...
If of course you want to have factories produce/build supplies and PP, instead of making this kind of event... you just make an item, that costs more, and has it's own itemcatgory that factories can produce, but cities cannot. Pretty straight forward.