I have not bothered to say what I think the issue was even with my engineering and automation background because it would only be speculation without being able to see the disassembled components myself.
I don't think the issue is with the shock internally.
I think the problem was central to the rubber insulator bushing and backup washer that is on the bottom side of the upper spring mount. The bushing and washer fit inside a recessed pocket in the upper spring mount and can't be see after the unit is assembled. After thinking about how the assembly process in undertaken I think that IF the backup washer becomes misaligned on the shock shaft as the top compression nut is tightened, the washer could catch on the side of the recess as it is pulled into the recess. This could cause the washer to be deformed and damaged to the point that it does not back up and compress the rubber bushing on the bottom side of the mount as it should. Since it is pulled into the recess and would be hidden by the rubber bellows around the shock shaft the assembler would not know this has happened. The rubber insulator on the top side would look compressed as normal but this compression would be from the downward push on the shock by the coil spring.
Like I said this is only my speculation and I hope to find out for sure.
The fact that the shock shaft is not properly retained would not become apparent until the unit is installed and the weight of the truck is put on the unit to compress the spring at which time the shock upper rubber insulator would be able to decompress and the shock shaft would be able to extend upward from the mount.
No one else has responded to having the same circumstance with the shock shaft extending from the upper mount so this may not be wide spread.
I don't know what else might cause the clunk but my clunk is no longer there.