What do you mean by a two chromosome species? A quick google says pea plants have 14 chromosomes. I only looked because I had never heard of a species only having two chromosomes. Do you mean the traits he was selecting for only had two alleles?
Unfortunately, most modern genotypes and phenotypes in humans don't follow these patterns, and over the years, genetics devloped an entire vocabulary and physical model to explain them, although at a fairly abstract level. None of it made any sense to me so I follow the biophysics/molecular biology approach which tends to consider many more underlying physical details
There's a related story, https://review.ucsc.edu/spring04/bio-debate.html and https://review.ucsc.edu/spring04/twoversions.html which shows how different fields think about the genotype/phenotype relationship. Grinding up steering wheels to figure out how they work...