Gibby,
Doing overdubs at the church rather than in the studio? Hmmm!
I would say they were trying to get a fatter guitar sound and/or add some more EQ/EFX to your playing in order to get that dual guitar sound. Now the open string and distortion mutting is something you should have asked the engineer after the session. Those duds generally have a specific sound plan in their heads and will not tell you until its all done in post production.
Just be cool and learn from your first live recording and overdub session. Let the pros do their thing while you pick the string.
You'll be talking about it 40 years from now...