The dark part is a problem that's occuring in rev 104 (and possibly earlier versions), it's fixed in rev 120, but since that's not released yet I'll give you a solution.
Noggit completely covers your ADT in shadows when saving, however, if you save your ADT when it's filled in shadows, and you reload it, you'll see that the shadows are gone, do NOT save it again in this case, just insert it into an MPQ. Also a way to remove them all while building, but not using it again is to increase your brush radius to 1000 and reduce your brush speed to 0 with the raise/lower tool.
For the doodads, there's currently a problem saving them with noggit, however once you've saved your ADT in Noggit, open it in Taliis and save it again, it should work this way. Though they might be missing collision, but hey, they're there!