Third Sanctuary and Second Sanctuary should be included in the Dark Sanctuary section of the Leitmotifs article, as, while it's less immediately noticeable than the From Now On variant, the Third/Second Sanctuary Motif is, in fact, still a variation of Dark Sanctuary. The intervalic pattern of the arpeggios is identical, the first 2 notes of each phrase are merely truncated, and the first note of the second phrase is doubled up. If direct evidence is needed, I made a video that demonstrates it on this Reddit post.
The council (collectively referred to as John #wiki-discussion) has reviewed your suggestion and ultimately decided it wouldn't count as the same motif if the melody has to be deconstructed and re-arranged to get there. It may be included as trivia points in the second and third sanctuary's OST pages, though.
Personally, I don't really agree it's different enough to justify being categorized separately when variants like the version in From Now On, GUARDIAN, Ever Higher, etc, also needs to be deconstructed to get back to the original. There are only two changes (the video I made presents moving the notes back as a third step, but it really isn't, it's just that deleting the starting notes of each phrase truncated the remainders since the rhythm is restless.), and it doesn't even need to be rearranged at all.
But if it's still seen as too transformative to be included at this time, putting it in trivia would be a fine compromise.
I'd definitely invite you to join the Discord server if you want to bring the topic back up. Otherwise, though, the majority - which includes people who know a lot more music theory than I do - voted overwhelmingly against including it.
If a decision has already been met, I don't want to push the issue too much since it's not that big a deal, but I would be down to discuss it.
Not the same topic but related enough to go here:
Should we name the motif shared by Ever Higher, Crumbling Tower and GUARDIAN (probably Heavy Footsteps too but idk) the "Climbing Motif" or something like that? Probably not, but thought I'd mention it.