You are right, CopyPaste always works but for me scrolling, selecting text and copy/pasting 40-90 chapters is painful due to RSI joint pain in my finger.
Although CopyPaste can be done a few chapter at a time as you read, to spare those fingers. There were some books with layout/formatting issues that could not be fixed easily in Calibre. For those books, copy and paste was the only way.
Text fixes for books in Calibre was only a pain in the beginning when I had to learn the software and figure things out, issues in LingQ and work arounds.
The Calibre reader can potentially become a LingQ replacement with its content server and TTS and AI features in the reader and books management features. I think it is worth learning how to use it.
Recently when I discovered that one can save Search and Replace operations it is now just a 3-4 clicks for most books. You can even export those operations and share them with others.
I use open source Libation app for downloading my purchased audio from audible, it downloads by chapters too. It is just that sometime the chapter audio need to be split if the Kindle book chapter is more than 6k words or there are more kindle book chapters than the audiobook chapters. I prefer to split rather than merge to play it safe and avoid hitting LingQ 6k word limits.
Sometime there is more audiobook chapter than kindle book chapter, example the book Le Voleur de Foudre in screenshot below.
So for this book I had to split the kindle book chapters text to match the audible chapters.
I use audacity for sound editing too. Easy to use but it is still quite a bit of time waste to do all the edit.
The text fixes for whole book can be done in 5-10mins but all the audio stuff (edits, time syncs) can take hours sometimes.