Am I correct in assuming that your protagonist and main character are the same person? Because personal issues like self-esteem or a combative inner voice are definitely in the realm of the Main Character Throughline.
In which case I think you're asking if your Influence Character could be the voice in his head. Short answer is yes! The Birdman film with Michael Keaton does this.
Just FYI, the protagonist / antagonist represent the opposing elements of Pursuit and Avoid when it comes to the Overall Story Goal. It's a detached, bird's eye view of what ails everyone in the story. But the Main Character and Influence Character Throughlines represent dynamically opposed perspectives on personal issues. How these things overlap (i.e. is my MC also the protagonist, or does he have a different Story Goal function?) is up to you.