Ok this might be really dumb but I'm wondering if clean tone has an influence on how the distortion petals Distortion sounds?
There's probably a more detailed answer, but in short yes.

The EQ on your amp will effect the sound of your Distortion pedal. However most pedals do come with some kind of EQ adjustment (either a single "Tone" dial or multiple controls) to help.
Fender 60W Super-Sonic Head
Fender 2x12 Cabinet (Vintage 30s)
TC Electronics G Major
Boss Blues Driver BD-2 w/ Keeley mod
MXR 6 Band EQ
BB Preamp
Jim Dunlop Crybaby Wah

American Fender Stratocaster