Vol 3 is even worse! Oh gosh, it's so depressing. SPOILER
Since this is about destiny and fated pairs, does that mean the new guy is an omega that could be fated to the other alpha butler? So he's struggling cause his body's attracted to the new guy but his heart is for beta butler?? I hope I'm wrong, please.
as mentioned by others before, what you have said is correct regarding volume 3. But it isn't completed yet, so I guess even if there is an obstacle like that, Kudo and MIyauchi will still end up together.
I also think that author tries to convey to us two different point of views in omegaverse:
1. No matter how much one denies the other (or how much one denies his feelings/attraction he has for the other person) , the fated pairs will still end up together and they will still love each other. (In case of Aoi and Jirou)
and the other POV is:
2. No matter how much attracted you are to your destined pair, you will still try your very best not to give in to that destiny because there is someone out there who you truly love (who is not your destined pair). You will do everything to fight that destiny (being fated pairs) just to fight for the one who is really in your heart.
(And I believe that Kudo and Miyauchi are in this POV)
Yeah I thought so, too. The two sides of DESTINY. Even without translations, it was pretty obvious what the struggle was about. The fact that fated pairs are strictly between alphas and omegas plus the capability to give birth gives purpose to omegas, similar to how other women's mentality on fertility. It's depressing that this parallel universe created betas and were able to come up with this fated pair thing because I had the same question, what about betas? Do they need to just pair with one another because alphas and omegas would be bound by that "fate"?
Yet it is said in the first chapter that fated pairs is a myth but was debunked by Aoi and Jirou because it's true but Kudo and Miyauchi are going to prove that it is a myth, that in the end you are still in control of your destiny, you get to still choose who you want to be with, maybe.

Raws (in Thai)
http://myyaoitranslate22.blogspot.com/2017/01/kdv2.html (Vol. 2)
http://myyaoitranslate22.blogspot.com/2017/01/kda.html (Vol. 3-On going)
http://harmonia17.tumblr.com/post/157863810812/kashikomarimashita-destiny-spoilers