This is the same issue i was facing couple of weeks back, Product query works only for partial location counting. Problem is we are doing location level counting but for specific items to reflect on the work order you will have to break the work template line by item number. Only then the item numbers will be available on the work order.
Below is OOB config. do this for the work template you. It should work.
When you create a CC work you will notice the filter item numbers available on the work order lines, and the CC scanning happens only for those items.
