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Could you be so kind and explain where I can find this setting? I can only find the gain setting of the input at the Audio I/O page.
Sure! Click the Home button at the top or the Processing entry on the sidebar to find the Quick-Adjust page. This page has a Levels adjustment that affects the sound after the Repair section (so your noise gate may need to be adjusted if raising the input gain). If you add 6dB to the Input in the I/O, you will want to offset it by -6dB on the Levels pre amplifier slider.
This should do what you need without affecting the processing, allowing the Bypass to keep its gain bonus. I agree, it's not as simple and straightforward as a Bypass Gain setting, but the functionality is there. Maybe Hans will reassess this at some point.