Which X-Y chromosomes have the developmental genes for mammals?
First, while half the chromosomes come from each of the two parents, these two sets of chromosomes are not termed X and Y (they would usually be called maternal and paternal).  The terms X and Y refer to potential members of just one pair of the 23 pairs (in humans) of chromosomes, and X chromosomes can come from either the mother or the father.  The presence or absence of a Y chromosome determines sex in mammals.

The Y chromosome contains one gene, SRY, which determines sex, and almost no nother genes.  SRY simply switches on the "make a male" program in the cells.

Essentially all other genes, including any toolbox genes, come from both parents, one copy from each.  (An exception, in males, are those genes on the X chromosome, which in males are present in only one copy and which came from the mother.  Another exception is mitochondrial genes.)