You are in the right track. To actually make CRISPR/CAS-9 work for "reduce inbreeding" issues, we would need to understand how the whole animal genome operates

You are in the right track. To actually make CRISPR/CAS-9 work for "reduce inbreeding" issues, we would need to understand how the whole animal genome operates and all possible connections between genes and define what are the recessive genes that might cause some anomaly in the selection coefficient and decrease it. Without this map, how would we are going to be able to use a technique that alters genes and efficiently change nucleotides to avoid recessive traits?