I'm certain they still play the end of day music in the lower dome. I have the full track of this which is nearly 14 minutes long and I remember hearing the music from 3:15 onwards everywhere across the park, including the dome, underneath it, the bridge and the entrance throughout 2010-2012.
I don't think Thorpe have fully abolished the end of day music (yet), I can only guess some days it can be heard easier than others. Typically, every time I visit, I hardly hear the first 3 minutes of the track, only the rest of it from 3:15 onwards.
So I'm sure that the lower dome and end of day music are the same track, but due to the change in music at 3:15, that might explain why some people get confused that there are 2 different end of day tracks that play in the lower dome, or other areas of the park.