"Maybe just hard to rationalize"... 100% agree with that last statement.
I could understand resisting her advances if he was already in a relationship with a different person... but he's in a relationship
with her. I guess Japanese Culture is strong enough to overcome the urges and instincts to reproduce. Or he just has a very low sex drive to begin with.
While I agree that this explanation is the most likely... I also hate it the most because it stomps on the rights of the creator to freely express their story.
A few things, corporations in general controlling media is a global reality.
Again, one must remember that manga are STILL a commodity (serialized ones at the very least, Pixiv, Twitter, Fanbox perhaps less so, but still). Some of it is likely editorial restrictions, but at least as much is probably due to an authors desire to appeal to and be read by as large an audience as possible, and equally as likely to be the kinds of idealistic characters they want to write. (Realistic or not, I think the vast majority of authors would be hard pressed to write a good and widely accepted romance where the MMC just "jams it in" at the first opportunity, though ironically I can think of ONE good one, but it's decidedly NOT widely acclaimed) Be those reasons economic or personal, they still stand.
As far as Japanese culture goes, well, declining birthrates are real, and while it's quite a bit more complex than the scenarios in manga, obviously the culture plays a role.
A final note, having reservations about sex (when inexperienced and young) isn't particularly remarkable or unbelievable. A lot of authors choose to showcase more of the "good" side of the response spectrum. Inspire and uplift.