What does the allele indicate in this pair of homologous chromosome?

Homologous chromosomes are made up of chromosome pairs of approximately the same length, centromere position, and staining pattern, for genes with the same corresponding loci. One homologous chromosome is inherited from the organism's mother; the other is inherited from the organism's father.

not necessarily. higher fitness requires the organism to be reproductive successful. for example, an organism at age 10 with 15 offspring is much more fit than an organism at age 15 with only 5 offspring.