I am curious as to what differences you are seeing between the two lines are. I initially thought that I possibly had two lines of Phantom. One appeared significantly different than the other, even the babies. One of the founding animals I bought directly from RDR so I know exactly what that one is. The other came in a multi-gene male. I do not know where the male's phantom gene originated from but he produced clutches of animals that consistently showed a more refined, sharper, brighter animal than the RDR Phantom. That was up until this season. One baby out of about 20 phantom combos popped out that looked exactly like my RDR phantom. I have yet to mix the two lines, but I no longer think that the lines in my collection are different.
I have seen a difference in Purple Passion/Mystic Potions that I think is pretty consistent, but from my experience, It may have more to do with the level of darkness in the mojave gene. I will find out this season. I have a very light Purple Passion that I am going to cross to a very dark mojave (not related), and also back to his mother who is a very light mojave.