Don't forget that the software has to cope with a wide range of string gauges, playing styles and manufacturing tolerances - it is only to be expected that it will include some sort of dynamic compression before modelling. The global settings apply before this stage, so the trick is to get the level when that compression is minimised for your specific guitar, set-up and playing style without going too low in level and killing the resonating string on the sitar for example.
When I did this I was down at -7db on the lower 4 strings and -4db on the top 2. Then I upgraded the firmware and at didn't sound good at all. So if you do a firmware upgrade you need to reset the global string levels back to 100% and then calibrate them again.
I really wish that when connected to Workbench HD there was an auto calibrate procedure that allowed you to strum the strings as hard as you would normally do when playing loudly and for the software automatically adjust the level for each string to that point where compression is minimised.