As follow up question for this post:
How do I install global certificates on a Rootless El Capitan for mono?
Mono uses the path
/usr/share/.mono/certs, which isn't allowed anymore (see refered post).
Does someone knows where I could store those certificates other then
It is not a problem for us to install the certificates in the config folder, but it is a minor annoyance, because all new users on those devices will have to run the installer, instead of only the first user.