Your correct but there is the rule that both of them have to be in heat/rut to have a baby. I pray the author sticks to that rule.
That's not a rule or that common across a/b/o world :/ if you'll remember the doctor warned him to not get pregnant because he can. Doyun doesn't has to be in heat, he's still fertile just not as fertile and Taehan is at his most fertile with more chances of getting him pregnant. Particularly I would prefer the author waited, I don't want to see babies now either but there is in fact a good chance Doyun is pregnant.
That's why I said 'I pray the author sticks to that rule.'
It depends on where the author wants to go, I hope he gets an abortion.
That "smell different/comforting" is a big ass sign Doyun is pregnant. It's very common - mostly in fics - for the omega to smell sweeter and really good, especially to the alpha dad when the omega is pregnant. Not shocked though, homeboy Taehan not only knotted but came a lot inside.