Let me explain how the input and output knobs work.
If they are not linked, the are completely independent.
If they are linked, when tweaking the input knob the output gain will be auto-compensated automatically, but you can still tweak the output volume. So, you won't "see" the output knob moving but it's compensated internally.
The problem we had with they being hard-linked is that you couldn't make adjustments in the final volume of the signal, that's why in version 1.5 we changed the behaviour.