Turn off notification sounds and vibrations while allowing phone calls to trigger sound and/or vibration on Nexus 5
This is an issue I have as well, it lies with the apps, whose settings override the default ringer and vibration settings. In order to completely disable vibrations you will have to disable them in Settings > Sound, and individually in each app.

Twitter app you will have to go to Settings >  and there is a Notification Settings sections that allows you to disable vibration.

As an aspiring developer, it will be my goal to default to system settings but allow for customization, as it should be...