I'd like to see proof of this as well. Everyone likes to throw concepts like gene location (allele) around, and the only way to prove it would be to prove that without any doubt you could NEVER produce a Cinny Super Black Pastel or a Black Pastel Super Cinnamon.
Oh and to define my own terms we'd need to see breeding of Cinny Black Pastels together only producing supers (Black Cinnys, Super Cinnys and Super Blacks) and all of their offspring when bred to any snake would always be only one of the two traits. I think 100 snakes produced this way would remove any reasonable doubt.
Alternatively we could map the genetics of ball pythons out and prove it that way.
Similar to the whole Lucy Complex and Lucys being produced from Phantom crosses, even though the Phantom's super is entirely different. Again we'd need to see if it were possible to produce a Super Phantom BEL the offspring of which being Phantoms and BELs and the offspring of the BELs being Phantoms and whatever the other morph was that was in the Super Phantom BEL.
I'm not trying to be a nay sayer, but there needs to be solid evidence to support claims of traits existing on the same gene locus.
As the snakes go, no. However I just want to say that on a general genetics level it is usually better to increase the line. Certain mutations appear over time (and we've formed some cool ones but it's not those that I speak of) and if you continue breeding within a set line without bringing in diversity then you increase the likelihood that negative traits will appear (Hemophilia is the commonly quoted example).
However there does exist an issue in this, you can breed with a line that has kinks and end up having that deformity exist in your own pre-existing line. The goal of creating more genetic diversity is to reduce negative recessive traits (or even dominant) however some offspring may still have this and it may not be lost. Through diversity you can introduce even new issues (sickle cell anemia being a decent example of this).