I agree with everything you said, especially the last part.
Yeah. Munetaka fell for Ayato, but because he was brought in to just produce an heir, he feels anxious and afraid Ayato would leave him. To him, bonding is an insurance that he won't. He is not against Ayato working because omega shouldn't work, but because if he stays home no one will take him and maybe Ayato will come to love him eventually.
Ayato doesn't want to bond because he's scared, which is valid. But he doesn't communicate that properly. And him always rejecting Munetaka feeds into Munetaka's anxiety.
It boils down to the old good communication. They should just sit down and calmly and honestly explain their points of view and feelings.
And I also agree that most likely an attack on Ayato will happen and Munetaka will swoop in like "I told you so"...
When an alpha much bigger than you pins you down and talks about a permanent mating bond all while your kid is watching. It's understandably terrifying.
Talking about a bond shouldn't be done like that, but in a civil manner and agreed upon without heightened emotions blurring judgment.
I guess seme is just a little more traditional considering he was brought up with love from his parents. He believes that an alpha would look after his omega, that marriage is (regardless if arranged or not) permanent especially once a kid is created through natural process (again, he believes there was a spark leading to mutual connection since that day). He believes that with all the things going 'right', it was only natural for the bonding to happen sooner or later.
There's nothing really wrong with that, these type of people tend to be the caretakers or the provider types of spouses, but if you pair them with a spouse who thrives on independence, who has lived their life in constant scrutiny and judgment, it won't be easy and you can never force them to "settle". These people have to choose for themselves on when they can accept that type of affection because if they let someone else decide for them, then they've fallen back to the very thing they've always wanted to escape from.
Again, I just think such things between couples have to be discussed privately, and especially away from children's eyes. Children observe very deeply and learn things through patterns and can recognize distress (though lowkey that baby looks like it got 2 braincells on vacation).
I'm going to guess that someone is going to try to assault/mark the uke and that becomes a turning point. It's the common yaoi trope anyways, but there's a small hope in me it doesn't have to be that way and that the seme and uke get to discuss it with no other external factors affecting the decision.