Seems you could fold the Khyber-mark feat chain into a standard Dragonmark feat, and just have it as one of the available types with the disposition modifier built in to the mark. Since characters can only have the feat once it removes the need for "you cannot ever gain dragonmark basics".
Khyber dragonmarks enable a different set of secondary follow-on feats, so the seperation should pay off soon
. Khyber marks are also slighty more powerful - allowing mix and match spell selection from a much wider range of choices than a single house-mark, ofset by not being able to take up to 6 feats granting greater depths within a single theme. Its sort of a "the darkside is faster" thing.
What does a "Your dragonmark skill is the same as for a ‘normal’ dragonmark of that type." actually do? None of the feats reference "your Dragonmark Skill", unless that's a futureproofing thing (for ExCs and MCs)?
There is a seperate section in the Eberron conversion document that tals about spell lists, casting, and dragonmark skills. I didn't include it here, beyond the "see page XX" reference.
Also, is it just me or are there echos of
constellation Astral Magic (and is this intentional)?
As the astral magic system came from mixing Eberron inspiration with Mastercraft mechanics, its not surprising a more direct addaptation of the inspiration would look similar