Ok after extensive testing (Like 4 hours) I've finally figured out how to use this mod to sort by mutations correctly.. I have to say it is Extremely unclear KAVAN..
I want to leave some instructions for anyone else desperately looking through comments like I was so as of this date here's what I figured out. Also Im tired and rushing this so excuse how sloppy it is..


HOW TO USE TO SORT EGGS FOR SKILL MUTATIONS

1)Place devices and set range
The Hatching/Butcher device Must be within Breeding devices range or else breeder will not send eggs to it.
It will take All eggs dropped no matter the source.
*Be aware that if egg hatches within the Hatchering devices range it will be tamed IF tamer is set otherwise it will not tame*

2) Enable sending to both devices & Customize settings as desired (such as egg auto dropping)

3) Set DESIRED number mutations and make the other side greater than 0
So if you're going for 20/20 mutations on the paternal side like I am it's simple..
Make "Current Male Mutations to look for" to the Total number of mutations you want on your paternal side and make the female side 1.
*If "Current Female Mutations to Look For" is 0 it wont work and they all go to Hatching*

I'll come back to this post after some sleep but this worked for me