That is weird. All 3 peppers plants would not put out pods in the same way. In my experience, temperature does not really change the shapes of the peppers. It would cause flowers to drop or pods not to develop. Sometimes, the first group come out different than the second group. Year to year, peppers do not always produce the same traits. Sometimes, 1 gene gets left out and it changes 1 little thing. Its also possible that they are crosses but if this is the first batch, that my be your answer. I have some Choc habs as an example. They both produce elongated pods, 1 dark green pods, 1 light green pods, both from the same plants with round pods. 1st batch so Im thinking it is from that and not a cross. I believe this may be what is happening with yours as well.

It looks to me like you may be under watering and it has too much fertilizer salts in the soil, this could be caused by water with a high PH or fluoride in the water. They are very susceptible to fluoride poisoning. You should probably flush the soil. Most houseplants with the exception of cacti like the PH to be below 6.5. Take a hose and flush the soil for about 10 minutes or put it in the shower and let the water soak the soil. Let the pot drain and put it back where it goes. I would then start using distilled or rain water to water it. 1 cup a week doesn't seem like it would be enough for a plant that size either. You should be watering enough to flush the soil of salts. Also do a search of the forums. I'm pretty sure this question has been answered hundreds of times through the 20 or so years GW has been going. You may glean something that I've forgot.

What works for me is to put the plant in a bucket and fill up to the soil line and let it soak for 15 minutes or so. Lift and drain taking note of the heft of the pot and don't water again until appreciably lighter. You also could use a pointed dowel to check the soil moisture. My Dracs can go two or three weeks between watering with this method. tj

It's possible that your scion (Rainier) is outgrowing the rootstock which gives the dwarfing you purchased. But this appears to be a young tree; if I use the grass as a comparison. If it's young make sure there is no tape, for instance, girdling the tree which may kill it. It's also possible that the scion was larger than the rootstock when they were grafted. But if that's what happened I wouldn't know how the graft was done. It does appear that the graft union is not much above the level of the ground.