The only general input/output gain settings are instrument/line level operation. You can probably leave these at the default instrument level for your setup.
The Program and each Preset all have input/output gain levels, can you please make sure that these are all at 0 db? It can be easy to not realize that a Program gain level is boosted or cut.
Press the Parameters button a few times to see the different parameters for the Program and each Preset. Use the Select knob to scroll through the parameters until you’ve made sure that all of the input/output gains are at 0 db.
You should also make sure the mix of everything is set to 100%. A Mix level of 50% can have a perceived volume increase because it is the full volume of both the wet and dry signals.
If you try all of this and still find that there is a perceived volume increase, please try using just the H90 and an amp without the switcher and let me know if you experience the same thing.