Each Ford design engineering group had total custody of its base number assignments. (At Ford Aerospace, we called it "creative part number engineering".) When a different design was introduced for a part, in this case the "Lower Back Panel" (we call it the rear valence) a new base number was used. We don't know all the intricacies involved here, but 1964-66 Mustangs used base number 40544, 67 Mustangs used 40330, which was then changed to 40544 in a design change scenario. It's not unusual to change base numbers, Ford did this a lot (yes it is two words) in the transition from production parts to service parts, mostly to consolidate similar parts. They understood it and made it work. Just believe.
Jim