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So I tried many things.
The only way I could run koreader efficiently at boot was to run it last, after nickel.
Then it works perfectly. And kills a few processes in the way.
I have now a Foss koreader e-reader, that runs without the kobo software, running from a full ext4 system.
The system as a whole is significantly faster.
And I can have symlinks, which transform completely the way I handle my huge collection of ebooks/pdf/Mangas, etc.
Thank you guys for the pointers.
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