My guess is that it just has to do with the quantity made. You couldn't get these at all for a while (while they were correcting their problem with dampers), then they made a batch for repair parts. Apparently it was a small batch and they are trying to get their cost of retooling out of it.
The 3.0L was used on a lot more than just the LS, T-bird, and S-type, so its tooling cost is spread out a lot better.
(Again, this is just a guess, there doesn't seem to be anything special about the 3.9 damper.)