Hi, I noticed that the Hexcrafter is treated like he has the Witch's Hex and Major Hex class feature, this allows him to take any Hex-related feat like "Extra Hex" or "Accursed Hex" which have as a prerequisite: "Hex class feature", but he can't take any Major Hex-related feat because PCGEN sets two prerequisites:
Having the Major Hex class feature: which the Hexcrafter meets;
Be, at least, a lv 10 Witch: which the Hexcrafter doesn't meet.
In that case, the Hexcrafter should be prevented from taking any Hex-related feat and not just prevented from taking any Major Hex-related feat.
I attached a file with an Hexcrafter lv 12 for you to test this if it helps.