No problem, Brody. I was scratching my head that you really seemed to believe that was the REASON the scene was dark. Meanwhile, a very interesting story about filming indeed.
The reason the gazebo scene is dark between the Captain and Maria for "Something Good" was because they couldn't stop giggling. Julie Andrews has talked about it frequently. It wasn't intended to be done in silhouette, but neither one could keep a straight face. So they re-lit the scene right there on the spot and filmed it the way you see it in the movie. I should add that it was one of the last scenes shot (the very last one was Sixteen, Going on Seventeen on the same set), and everyone was dog-tired, overworked, and behind schedule. They couldn't wait for Andrews and Plumber to "calm down," and they couldn't reschedule it for another day. It was a quick fix that actually looks wonderful in the film.
EDIT: As for Peggy Wood, her lip-syncing was fine, but they worried about it. She and Wise also both worried about the transition from speaking to singing, so they had her turn away as the song begins. But she is definitely seen lip-syncing on camera in this plus How Do You Solve a Problem Like Maria? and she does a fine job of it.
It was also Wood's decision not to sing the role, even though they cast her hoping she would. She didn't feel she could hit the high notes well at her age, so she never even attempted a pre-record. With Plumber, he actually did the pre-records himself, then he and Wise together decided to dub the Captain's singing after they did a test. Plumber wanted to try it himself first, though.
"Jaws is the Citizen Kane of movies."
blocked: logan2, Diamonds3, Hamilton22
In addition to what best12bars wrote, Wise thought it would be pretentious and kind of cringe worthy for the Mother Abbess to start singing the song right out to Maria (works on stage, but not on film), so he had Wood turn away from the camera when the song begins.
The last big scene shot was indeed Sixteen Going On Seventeen, but the unofficially last scene they shot, aside from the inserts of the frog and pinecone scenes, was the scene where Georg, Elsa, and Max were coming back from Vienna in the Mercedes.