I have almost sorted out what is going on with Helix input and output levels by my and my friends research. The professional standard for line level audio signals is +4dBu.
If we assume 15dB headroom to full scale digital level (0dBFS) is the standard Line 6 has adopted then Helix has three level settings:
Line level: +19dBu full scale (+4dBu reference with 15dB of headroom)
Instrument level: +11dBu full scale (-4dBu reference)
Mic level: +8dBu (-7dBu reference)