I hope they determine why fullscreen is preferencing the playing of 2D scenes first.
If I had to Venture a Guess.
The Software is encoded to use it as the First Scene, because it is the First Official Scene that is Part of the installation.
Only if it is Disabled or doesn't exist, will a different Scene be selected as the 1st scene used.
I believe, if you want to use it as a scene selected at random from your other scenes
you should make a copy and give it a different name.
then Disable the Official one.
Don't delete it, as it will be re downloaded and installed again.
I've completed a round of testing.
I used several of my Own Scenes in various Folder names.
If I rename one of my Scenes to Background 2D
then that scene is selected as the 1st Scene used.
when there does not exist any scene named Background 2D
then a different Scene is used as the starting scene
So that pretty much validates my suspicion.
Just Disable to Official Background 2D scene
and if you still want to use it.
Make a Duplicate copy of it, and give it a different name.
The Copy can be in the same folder as the Original one, just give it a different name.