What governs if a sequence applies to physical traits or behavioral traits? Is there any rhyme or reason to the coding to signify what they represent?

Ehem, sequence don't govern the one or the other. What they do encode are RNAs of which a subpopulation, the mRNA is used as a template to form proteins. The latter are the movers and shakers. This is of course quite a simplification. And in the end, there is no clear distinction between physical and behavioural traits, given the fact that behaviour is a function of the brain, which is basically a physical entity.

I would also add that it depends on a) where the gene in question is expressed (the cell type), b) what the effect in said cell type is and c) the level of expression, whether it is basal or cell specific and thus a higher level of expression. Additionally you may have alternative exon splicing depending on which cell type the product is being in expressed in if it is a protein product rather than a functional RNA.

 

You also have to take into account the complex interactions between the gene products within the cell and how they respond to cellular signals. It definitely is not a case of one gene for one trait.