Also, how do you know that CIS went right to D1. Even the Cinefantastique article, from what I've read of it in regards to D1, seems to be saying that Digital Magic did have D1 decks at the time, but there was no specific mention of TNG actually being edited on them.
The archive of the Official Fan Club article I linked to says Post Group started using D1 for post-production in Season 4.
They list the equipment in the next paragraph of the article after the one I quoted. It includes Sony D1 decks.
So I don't know what happened, if anything, when they moved to Digital Magic.
It could also be that for some reason Unitel provided D2's of the film scans, while it was then edited on D1. This would still make some sense, since editing in the higher quality component color realm would at least help to reduce errors with bluescreen compositing, etc. But the initial source data would still have been composite video.