I managed to do this.
The object on which i was editing the value was CDO (Class Default Object).
Here’s the example of how to change variable and save it in defaultengine.ini:
UMyObject* CDO = GetMutableDefault<UTeamsSettings>();
if (CDO) // should be always valid but just in case
{
CDO->Variable = FName("New value");
CDO->SaveConfig(CPF_Config, *GetDefaultConfigFilename());
}
Also, I had to change declaration of Variable a bit (globalconfig had to be changed to config - see OP).