The Vrijheid (Late) currently costs less than half what the Vrijheid (Early) does to purchase one without D-mods. I don't really have any experience with what the values in the ship data file mean, but I'd assume a ship's purchase price is determined by the "base value" stat, with the late variant of the Vrijheid only having a base value of 1,175 to the early variant's 9,000. Probably a typo and it was meant to be 11,750 I'd guess?
Loving the mod, though, its been one of my favorites to use lately.