I think there 2 options if I understood correctly:

1. You can use a pre-defined project template that has the file-type settings configured
2. If you want to change this programatically then you need to obtain the project settings and then under those settings use the file type settings id (depending on the file type) to change the values, should work something like this:

var studioProject = new FileBasedProject(@"{Project file path}");
ISettingsBundle settingsBundle = studioProject.GetSettings();

var settingsGroup = settingsBundle.GetSettingsGroup("setting ID based on the file type"); 
//you can get the settings id from the project file

settingsGroup.GetSetting("Enabled", true).Value = false;// update the settings value