For instance, changing the difficulty level of NPCs (addon "Skilled NPCs") using OXPConfig also changes the values displayed in the "Config for Addons" menu tree.
This is less to do with Library, and more to do with the fact that I added support for Library to Skilled NPC's, which should co-exist if both configuration OXP's are installed. However, more options are available through Library than through OXP Config, so if you have both installed, you should make Library your default place to change the config.
I wanted to configure the Navi MFD, but it only works with Library, so now I have OXPConfig and Library parallel.
You can have both Library and OXP Config installed - they don't conflict with each other.
If some other installed addon depends on CCL, can I remove CCL now, after installing Library ?
If an OXP requires CCL, it will still need it even after Library is installed. Library doesn't replace existing requirements, even though it is designed as a replacement to things like CCL. It must be specifically targeted by OXP authors in order to be used.
Why is it not available in the addons manager ? My suspicion is/was because of conflicts ?
I think there are two reasons (1) Svengali is giving the pre-DM release plenty of time to bed down and for bugs to be discovered, and (2) Getting time to do the work required to do the upload.