I’m running a docker setup where my actual nextcloud server must be a “throw away container”. This makes it crucial to use a “custom_apps” configuration in my installation, so a user won’t loose all his installed apps everytime the container gets thrown away…
As soon as i configure a custom_apps folder - nextcloud starts to install everything into this path. This works fine for custom apps of the customer (i can throw away the container, make a new one, they are still there…).
But the problem is - when i update an official app, nextcloud will put the update-data for this app also into the path of “custom_apps” - and obviously it still looks into “nextcloud/apps” folder as he continues telling me that my app is out of date 
I have no idea how to work around this, as it seems to be a bug in nextcloud itself 
Just configure a named volume in docker as explained in the installation doc. No need to configure a special custom_app folder.
But the strange update notification might indeed be a bug unrelated to the Docker setup.
sry my description was maybe unclear - named volumes, that’s exactly what i’m doing… when i read over the docs again, what i missed is to point it directly into the same path as nextcloud expects (/var/www/html/custom_apps)… and ended up hacking a symlink to point my mointed volume into /var/www/html/custom_apps… which is in the end the same thing…
but yes - the thing about the sticking update notification is what is bothering me
Have you tried installing it the regular way? I simply have one named volume for the entire Nextcloud folder (/var/www/html/), like explained in the installation instructions and that works fine.
I suspect having the same folder in the main volume and also in another one (your /var/www/html/custom_apps) might be causing the issues?