Considering the genetic makeup of homologous pairs, will cells at the end of Prophase I be genetically identical to each other?

The correct answer is: no, the homologous pair will not be identical to each other.

This is because the alleles on each homologous pair are not necessarily identical.

Also, during the prophase I the exchange of genetic material between 2 homologous chromosomes non-sister chromatids occurs. That results in recombinant chromosomes.