If you don't change the settings on your amp when you change guitars, I think there is no advantage to using either guitar.
If you do change your settings when you change guitars, you will likely want to create more than one profile, to suit the different amp settings.
Some (even if only a few) would say that certain guitars or pickups can result to slightly different results in some nuances when it comes to refining. I've conducted a few such tests before and noticed slight differences in results that could suggest such a thing.
That said, attributing this to the guitars, pickups, tunings, or just differences in how refining worked -- it's not so simple to know what causes what, unless testing is more nuanced.
It can even be that someone just happens to focus on different playing styles while refining with different guitars or tunings, altering results... Though refining has gotten quite a bit better later on in the product's development and/or maybe first stage of profiling gets closer now, lessening the chance of this happening anyway.
Saying that, kemper's position has been that guitar used does not make a difference, from what I remember. Do not take my words as "official" advice or something of that sort. I also know mods don't want misinformation spread about Kemper -- and rightfully so.
What can be said for sure, on my part, is that how you set the source tone in regards to the guitar, tuning, pickup, and what you want to achieve may result to profiles that don't work well with another instrument, different tuning, or after replacing a pickup on that guitar. Surely depends on one's standards, expectations too, how much such differences matter.
That's not about profiling accuracy though or nuances being slightly different due to different guitars used in refining (or whatever the causal link could possibly be, if any at all). It's just about setting the source tones as based on the signal, how it comes out of a guitar 
A further note: it's probably cool to make profiles of different gain levels. While at it, it can also be interesting to find a particular preamp gain level you like from the amp, and then play with the gain control on the profile.
Lessening the kemper gain control can allow for some cool stuff. In my experience it tends to retain characteristics of the tone not comprised of what people would call "distortion level".
The real amp may change character in different ways as you lower the preamp gain. That can sound good, sure, and he profiled anyway, but there's a chance you discover a tone at higher preamp gain settings which when profiled, lowering the profile's gain later, results to more of the tone you are after, just at the right gain level.
That could also sound better with some guitars than others, in a way. The amp itself would likely not be able to achieve the same result easily so, if at all, depending on the case.
There's a lot more to say, but would go into different profiling topics too much. Good luck.
