I have to add treble, presence and bright on every patch I build...and, I do quite a bit of amp tweaking in the advanced settings to get a brighter, crisper sound.
My tones are not muddy or dark after I tweak them.
The stock patches sound quite dull and muddy to me...and I'm using EMG 81/85's and T598's on all my axes...
My setup:
Axe FX Xl II Plus
Matrix GT1000
Xitone 2 x 12 passive wedges
When I crank it up, things change dramatically, and the tones get much brighter. It just takes quite a bit to drive these FRFR's...
So generally, I'll build my patches with some volume, because if not, they will be too bright when I crank them up.
My typical amps are Marshall, Friedman and Mesa, using the stock Mesa and Marshall 4 x 12 cabs most of the time. I play mostly metal and rock.
I have noticed that the clean patches are fairly bright on their own.
If I think about it though, on every tube amp I have ever had, I've had to increase the brightness, treble and presence...so this is no different.
I often asked myself if it was normal that all the stock patches sounded so dark and muddy, but real tube amps were never much different; I just forgot how they sounded.