First thought is kind of want to dispel any negative ideas someone might get from this about the grower. Pods for food / produce are not generally grown in isolation because there is no reason for it. A few people, like myself, give a bit of credit to the folk lore that says the fruit can look different after a cross pollination but that is instantly visible. Also, most scientific discussion says this is impossible as the fruit's genetics come entirely from mama.
Thing is, I do not think this is the result of cross pollination with another pepper. Find the video by Buckeye Peppers where the owner explains the variation rate in the Carolina Reaper is smaller than other peppers. He points to the tiny number of plants that did not produce the classic pod shape and describes them much the way your pods look. I have also seen variations, in my case chocolate. This is what I -think- is going on with the Carolina Reaper and its rumor of being unstable.
I -think- the pepper has recessive genes for a few things like that pod shape and being chocolate. As long as it self pollinates, the seeds that it produces will wind up looking like mama. However, if mama gets pollinated by another Carolina Reaper and both mama and papa have the recessive gene for that pod shape or the color brown, then the offspring show the recessive trait. I do not think this is the same as being unstable but I am none too sure the term is defined.
In any case, I think the Carolina Reaper is new enough that we can expect lots of variations to be identified and grown out into its own thing. Think about the wild wild west sort of thing that happened with the original 7 pot variety was first being bred. This strain, that strain. Gotta figure the same will happen with the Carolina Reaper. Its what we do. I say instead of discarding the thing, grow it out and see what it becomes and many congratulations on having the opportunity.
I frigging LOVE surprises... well, as long as it isnt every damn seed in a batch. Then I get all grumpity. You wouldnt like me when I am grumpity. I wind up naked in strange places.