The title of what seems the original request in 2018 for the ability to "custom" sort notebooks is misleading. Using the implementation of this but for notes, "custom" means being able to sort manually at will. However, only sorting by Title and Date was implemented in the end for folders, and the issue was closed on Github, although calls for "manually" were also part of the discussion.
Plenty of requests have popped over the years on the forum. Is "custom" ordering in the pipeline at the moment?
This could even be considered a usability issue. You can move subfolders to other folders by dragging and dropping them which misleads the user into believing they can also place the folder between others on the list in the order they want.
In fact, an older thread on the forum even posted this as a UX issue not knowing it isn´t a feature to begin with. Made for some awkward misunderstandings on that thread.. The user thought it was "difficult" to reorder folders because when trying to place a folder above or below others on the list, it ended up inside one of them. Truth is, you can't place them at will at all, just move them from folder to folder.
Goes to show how it´s a feature congruent with how the UX is currently presented. Users intuitively assume it works that way.
I landed here from Google because I was sure this feature would've been in already. Notes can be ordered manually and notebooks can have their own internal sorting method, but somehow the manual ordering of notebooks themselves remains impossible. I wanted to try adding visual separator notebooks, but that's only possible by prefixing them and all other notebooks with numbers. It technically works but it's sure as hell clunky!