Godot version:
3.1 stable
OS/device including version:
Linux Kubuntu 18.04 -- irrelevant
Issue description:
The option "make scene root" does not what it is intended for, but follows the semantic of "Make scene root IF there is no root scene already defined" ;D
Steps to reproduce:
1 - create a project
2 - create a scene A
3 - set it as root
4 - play --> it runs scene A
5 - create another scene B
6 set it as root
7 - press play -> it will still play scene A

As a workaround we can still change main scene from project options:

It is a minor bug for this GREAT project.
--R
You are probably misunderstanding what this option does. It's supposed to make selected node the root of currently edited scene.
E.g. making ChildNode the root in this case

will produce this

It works as intended.
It is a misunderstanding, but I think the root node should not have this option.
Thanks for the explanation @KoBeWi and @vnen .
Glad to see that Godot community is such a nice place !
-- R
Most helpful comment
It is a misunderstanding, but I think the root node should not have this option.