So to play Devil's advocate, if someone wants a custom order and you have the buy the entire pack of beads, then shouldn't your price cover your losses? What if you are unable to use the other half of the package?
I do a lot of custom orders for other things and, if I need 1 yard of material, they pay for 1 yard of material. If I can get other things cut from the scraps, that's a gain for me but I don't charge less for the custom order because of it.