Hi
I made this proposal over one month ago* and got a quick reply, explaining that the problem did not present itself in the same terms for Koreader than for, say, Calibre or Sigil. I was unaware of it.
So, I looked for more information, which took me some weeks (I'm slow) trying to see if this problem could be circumvented. I found a way that has been used by Prince PDF and that could be of interest and posted it.
https://github.com/koreader/koreader/issues/5821
As the initial post and its reply have been published a long time ago, I am not sure if my last post will ever be read. Hence this post here.
* There had been some similar proposals already some years ago.