With the album's storyline in mind, this part takes place near the beginning. Twilight has just become a Princess and gained wings, and she is very daunted, excited, and nervous about her new title. It's all very new to her, and though she is a little frightened by it, she hopes it'll smooth out once she gets over her fear of not living up to Celestia's wishes.
As far as I've bothered to look, the mare in the moon head permanently disappears after Luna returns, leaving only generic craters on the moon's visible surface. Luna herself superimposes her silhouette over her moon in 'Sleepless in Ponyville' to directly communicate with Scootaloo - the filly she was helping overcome her fears that night.
Twilight's a big girl now, has been for a long time, she doesn't need Luna to get so "biblical" towards her hehe.
Plenty of fantastical elements left, and plenty more are appearing. Rainbow Falls, airships, weather factories, the 'fact' that rainbows can have their colours vacuumed out by three fillies. Just gotta keep your eyes and imagination open and you'll that its not just a tree and a moon that makes Equestria so fascinating.
I understand, but they were episodical and such ^^ That tree was pretty special, not because it was unique to the world, but because the viewer may have developed a certain attachment to this piece of backgrounf ^^ But yes, they have an intriguing world