To reproduce:
1. Open the "UnityPlayOnAwakeBug" scene in the attached project
2. Select the "Trigger Source" Game Object from the Hierarchy
3. Uncheck the "Play On Awake" in the Inspector in Audio Source component
4. Play the scene and press "P" to hear how audio should sound
5. Stop the scene and check "Play On Awake" in the Inspector once again
6. Play the scene and press "P"

Desired outcome: Audio clip sounds the same as being played with "Play On Awake" unchecked.
Actual result: Audio clip sound is significantly louder when "Play On Awake" is checked.

Note: The issue seems to happen only when there is no AudioClip attached in the Audio Source component (when AudioClip is called from another script).

Reproduced with 5.5.4p1, 5.6.0b3, 5.6.1f1, 5.6.2f1, 2017.1.0a1, 2017.1.0f1, 2017.2.0b1

Update: The issue is by design, because when there is an AudioSource that has no clip assigned but does have a MonoBehaviour implementing OnAudioFilterRead, it will instantiate the OnAudioFilterRead as a source when the sound is started either via the "Play On Awake" flag or a regular Play() call. When “Play On Awake” is off and Play() is not called, the PlayOneShot call will instantiate the OnAudioFilterRead as an effect that filters the signal mix of the one-shot sources.