Female Custodes actually make sense in the long run as Custodes were supposed to be the New Humanity. The apex and dream of what we could be. Free from the Warp and superior to everyone around. It makes sense that The Emperor would want them to breed with each other. Sisters of Silence are a mutation. A loyal and useful mutation but not something you want in the general genepool.

Space Marines like Thunder Warriors were always meant to be exterminated with select few Primarchs allowed to live out their days and help the New Humanity. Thats why Custodes hate Marines. They ruined everything and were supposed to be gone by now.