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DNA and Wonky pods

If you have grown peppers for any amount of time, you have seen what I call a wonky pod.  I am not talking about when a whole plant is just plain wrong and you scratch you head about your labeling system or wonder about your seed stock.  I use the term wonky pod to mean a single or small number of pods on a plant that aren't right when the rest of the plant throws fine pods. 
Where do you think wonky pods come from?  According to most growers, the pepper / pod gets all of its dna from the mother plant. So it seems we have two choices.
1. DNA flaw / mutation - I understand this is actually fairly rare because most flaws and mutations render the seed infertile.
2. Natural Variant - Seems a little bit more likely since the wonky pods are often described and found by others.

3. Growing Conditions - Maybe during the development of some pods, it was particularly dry, wet, sunny, or cloudy.  But during the initial development others, not so much.
Myself, I like it when I find wonky pods because they give me something to experiment with.  I am kind of leaning towards growing conditions because most often if I save the seeds from a wonky pod, I get normal plant without wonky pods.  Now if a whole plant has odd pods, its seeds tend to grow the odd pods.  But when it is just a handfull of pods that are wonky on a plant, it doesnt -seem- to have anything to do with dna.

So I guess the real question is do you think it is worthwhile to experiment / grow out the wonky pods?
Natural variant. A DNA mutation would be extremely unlikely, not just because it might render the seeds infertile but because it would need to happen when the branch is being formed, and then all pods from that branch would be different. That isn't to say it's impossible though, as yellow apples are all clones of one branch that happened to produce yellow apples on a tree that made red ones. That being said, other people wouldn't be likely to get them as well, and people do. Growing conditions seem unlikely just because I've seen differences in two pods started at the same time.
On mutations though, I have a Carolina Reaper that was a conjoined twin at the base, though one half of it died now because of aphids. It produces a lot of double flowers, but most of them fall off and in others only one half sets fruit. Never seen a double pepper from it.
Cuzzfish, maybe I just learned something.  Were you using apples as just a random example or are you saying that my yellow delicious apple trees are all genetically identical and came from a single clone?  If that is the case, I think I now more understand the need for cross pollinators.

I planted my delicious apple trees red, yellow, red, yellow to form a line that I hope will eventually be a wind barrier and provide a new shaded area.  That and for apple pie.  I do not remember if it was the red or the yellow that needed a cross pollinator but I think it might have been the yellow.  If all yellow have identical dna, I could see how it would produce more when exposed to a cross pollinator.  I imagine that if it is all the same dna that bad genes meeting up would occur more often.

Am I close to understanding the need for cross pollinators in some plants?