a "Custom Order" or "Custom Slot" normally refers to a product in an online store that has not been made yet. It will be custom made to suit the customer (Often from a range of preset options). These are often highly sought after, particularly if a pad maker only offers these rarely due to other commitments.
One reason that some sellers prefer to work with instock pads only, is because it can be more time consuming to make individual pads for customers than it is to make several pads at once to put in the store. However custom orders allow the customer to receive pads that are tailored to their likes and needs.