I seriously doubt Century Arms assembled any M39s. The parts were a mixture of Russianicon/Finnishicon parts to begin with, plus during WWII many of the rifles were damaged/cannibalized to keep others going. After WWII they would have refurbished. Later on the Finns themselves used up what spare parts were remaining to build some in the 60s-70s.

If the bolt is mismatched it is likely because of importation and simply not having the bolts returned to the original rifle (like most mismatched bolt cases out there). The other mismatched parts are likely due to refurbishment as I suspect they weren't spending much time on renumbering everything rather getting it back to functional condition.