I came across this video explaining phenotypes. It is 6 years old and so it might be somewhat dated. But it may be a good start.
Neocardinia phenotype explanation
He also highlights the color changes related to substrate color. He ties that response to epigenetics. Very interesting.
In watching my red cherry shrimp it seems like they have different personalities. Some hang out behind the filter where others flit around all over the tank. Now is it that some are ill? Gender behavior differences? My imagination? Or personality differences? Well I found this recent study that gives a nod to red cherry shrimp having different personalities 
Study on red cherry shrimp personality What do you think?
The study uses the term heteropodia rather than davidi - what is the difference in any between the two classification terms?
I breed mine completely different then everyone else iv been “playing” with the genetics. Iv got reds that I mixed in a skittles tank. With some orange and yellows. Now that ended spectacularly for the most part. I now have all kinds of shades of orange yellow red and chocolate in my tank. I do have clear ones as well but I move them to my 29 community where a series of odd events took place. I specifically took the absolute most washed out ones in hopes to get a totally clear shrimp they started to turn by gen 2-3 the most vibrant Bloody Mary red. No idea how or why because they were wild wild color. Back to my skittles tank. Mixing the yellow orange and reds seems to give me a stunning variety of rili colored shrimps. Or as I call them my cows. They have not uniform spots of color on them. They stay solid for the most part like yellows will be spotted white and yellow and reds will be reds and white etc. I even have had a few blue??? Or iv been noticing at least one female I feel has the blue gene in her because I’m starting to get blue babies after adding 2 new of each color. It kills me how a lot of people grade them because I use different cherry shrimp for different reasons. I originally moved the clear ones in hopes they would be a un noticed clean up crew not colorful. Then in my mainly shrimp tank my goal was to experiment with genetics. In a world of shrimp keepers telling me I’m ruining the quality I choose to find something new. I’m sure a lot of other people who kept shrimp were told they were messing up the gene pool mixing and matching them…. Now we have a never ending rainbow of cherry shrimps. So to me how to properly keep cherry shrimp is to simply enjoy them.
I don’t think you are off the mark at all breeding the way you do. Aquatic arts is breeding and selling wild shrimp, bringing back the shrimp to their natural colors. They are stunning.
In addition to substrate, food, background, I found info that stated low lighting will also help darken your shrimp.
On another note, it seems that a higher flow tank makes my shrimp happy. After I added an air stone to the tank, along with the filter set at high flow, my shrimp population exploded. Population explosion in my RCS tank!
