Hi Sebatian,
Regarding how the amp (profiles) distort based on the output of the pickups:
One route to go is to simply treat the kemper as a regular amp and accept that the difference is there and work with it - ie. accept that some guitars drive the amp harder than others
Another is to store input settings on the kemper, where you can adjust the clean sens and distortion sens for each individual guitar to get them closer in how they drive the profiles. You simply adjust and the push the "store" button. Also remember to "lock" the input section, otherwise the settings will be lost when you change profiles. You recall input settings by turning one of the knobs above the display (I forget which one).
Regarding the loudness/output of the kemper (output stage):
I believe you can do the same as option 2 above, but for the output stage. Keep in mind that there is a lot of parameters in the output stage (EQs for different physical outputs, etc etc etc...
You could also - in the output settings on the kemper - link the physical output you use to the "master volume" knob on the kemper. Then you can tweak that quickly when switching guitars. Keep in mind that this will change the volume of all the outputs linked to the master volume knob . The output section has a volume setting for each output individually, and based on where this is set "on the scale from low to high", I believe the master volume knob (if linked) allows you to make fine or coarse adjustments. I seem to recall that having a low setting on the individual output means that a slight turn on the master volume yields a large change in actual volume - and a high setting on the individual output means you can turn the master volume dial "more" before the same relative increase. Or vice versa. I may be totally wrong about this. 