"If there is a valid reason for not changing this" ... well, it is likely that you will visit the post and then check other answers for updates as well, thus spotting other new answers as well. Also, I think this is status-bydesign: only the latest of each type of notification for a given post is retained once read, to reduce clutter in a very frequently used tool. After all, as you noticed, the user activities page retains all of them in case you do want to see it.
For example, my inbox now contains one entry for three comments I received on some post, but earlier, when it was unread, there were three separate entries. The older ones of those were removed from the inbox after I checked the inbox once.
So, it's possible that when you checked the inbox the first time after the newest answer was posted, you didn't notice the entry for the older answer, and when you checked it again, that entry was deleted since it looked like you have already read that notification entry.