What is the genetic difference between two cone branches?
I don't understand your hypothesis. But the number of pairwise differences between two cells assuming neutrality ($\pi$) in the two different branches in $\pi = 2 \mu L t$, where $\mu$ is the somatic nucleotide mutation rate (around $10^{-11}$ on average), $L$ is the length of the sequence of interest (eventually the whole genome). $L$ can therefore be of the order of $10^9$. $t$ is the number of cell generation since the two cell lineages split. $t$ depends on the relative positions of the two branches but it could be $10^4$ cell generations. With these very quick approximations, we can estimate the number of pairwise differences as

$$\pi = 2 \mu L t \approx 2 \cdot 10^{-11} \cdot 10^9 \cdot 10^4 = 200$$