In my understanding, the author made Miya pregnant because it's what he wanted. He broke up with Kudou, not only because of the not fated pair whatever but because he learned that he couldn't get pregnant and therefore thought that their relationship will become meaningless since he thought he couldn't give Kudou a family.
I actually think Miyauchi being able to have a child was an important part of his journey. Miyauchi's struggle throughout the story was his inferiority complex with being a beta. He didn't believe that a beta like himself could have everlasting love with an alpha unless he was an omega. Aoi's marriage solidified that belief for him. Kudou defying "destiny" and choosing him as a life partner was one huge leap in Miyauchi's journey to realizing that he could be loved. Having Yuuichi was another big leap that symbolized how Miyauchi was just as good as an omega. That even as a beta, he can have a family, love, and happiness.
But also I'm extremely biased because I love cute parent+child stories. (▰˘◡˘▰)
Yes, it left a great impact on my heart and the manga focused more on the butler story, like give us more fluffy scenes please ╥﹏╥
The only thing I was troubled was about the pregnancy of the Beta, Im thinking that the author choose to make the Beta being the one pregant because if it was the alpha who gets pregnant, then it will lessen his masculinity
I know that people will say that all is well that ends well and wouldn't care if who was getting pregnant, but it was the actually conflict in the butler story, miyauchi [beta] couldnt be happy with the alpha butler because they are not soul mate plus Miyauchi was a beta, "not an omega"
I felt sad that he was the one getting pregnant cause what is his difference with an omega? there was about the soul mate problem, but they skip the problem about him being incapable of being pregnant
Anyways, I wrote too much, I just want to share my worry or conflict to the new readers who will read this Bl manga (づ ̄ ³ ̄)づ