Theoretically, Liquid Profiles should be pickup agnostic, especially if the profiling amp setting is:
Gain = max; and
The tone controls are all set to 12 o' clock
i.e. a sweet spot wasn't selected based on a specific guitar, which might have been SC or HB.
It should then just be a case of taking a Liquid Profile and tweaking the gain and tone to suit the guitar you are using - like you would for the real amp itself.
Whereas, non Liquid Profiles are snapshots of specific amp settings that the person profiling dialled in (and probably also refined) with a specific guitar. A Strat sounds different to an ES355, so these profiles will be aligned better to the guitar type that was used to set the amp gain and tone. Liquid Profiling (as I understand it) helps remove this link.
If I've misunderstood, it would be useful to hear from the Kemper team with any clarification.
That sounds pretty solid, like to know what Thomas dill thinks.