[Baertram]

>Remove the embedded libraries from the addons and use that standalone versions
Yes
But only if the libraries provide their own txt file!
AddOns provide the info the ingame addon manager needs via the txt files and the tags in it, like ## Addon Version to only load the newest version of the library.

If the lib does not have an own txt file (and I do not mean in the subfolder of the addons but the Library itself, here at esoui / in Minion) it might never had one and thus you need to keep it in the subfolder where it gets called by the txt file in the main folder of the addon (hard-coded call from the addon's txt file, not the library's txt file).

But in that case you should always make sure to download the newest version from esoui! Replace the files in the subfolder of the addons (e.g. /libs/CustomTitles) with the newest downloaded files.
If the library got an onw txt file on esoui/Minion you should delete the subfolders in other addons AND ONLY install that lib ONCE into your live/AddOns folder so that Minion detects it and keeps it updated. This is the very best practice.