Android ExtraPermissions doesn't work

Hey guys!
It looks like extra android permissions don’t work for me.
I’ve found some superfluous permissions in my final build (for example, READ_PHONE_STATE, GET_ACCOUNT ect).
After some research, I found that it comes from UEDeployAndroid.cs in case if I don’t have ManifestRequirementsOverride.txt file. So, as far as I don’t need those permissions I created empty override file. Now there are no permissions on my manifest. I can’t find even extra permissions from Android settings window.
As I understand, your script tries to find ExtraPermissions on the following file:
/Script/AndroidRuntimeSettings.AndroidRuntimeSettings
But I don’t have such file in the project. All permissions are located at DefaultEngine.ini
Is that a bug or am I doing something wrong? How can I use only my permissions from settings?

P.S. Of course, I can add all required permissions to ManifestRequirementsOverride, but I want to know proper way)