Why does allele linkage cause disproportionate phenotypic ratios?
I found the explanation at this site helpful:
http://www.ndsu.edu/pubweb/~mcclean/plsc431/linkage/linkage1.htm

I don't have a clear sense of what you mean when you ask about assorted phenotypes occurring before recombination ("crossover"). All of your examples deal with diploid organisms. If they are multicellular then the cells that can undergo meiosis are highly specialized, and eventually become haploid. As the chromosomes are prepared they tend to become compact, and are often not expressed. So it is difficult to assess the phenotype of those haploid cells. The rest of the cells in the organism are diploid  and at least some of them can express the alleles that give rise to the phenotypes that you are scoring.

At the moment of fertilization there is no further recombination, as the zygotic cells undergo mitosis.  There is no segregation, no independent assortment, no linkage (that you can measure--the genes are still arrayed along their chromosomes). Each mother cell divides to give two perfect copies of itself. Then the daughters divide, etc. Even in the cells that are going to become germ cells, they divide by carbon copy mitosis right up until they enter meiosis.

So there is no mechanism that would lead to genotypes different from the genotype of the zygote (until meiosis).