I just want to append my solution to the mentioned Article above.
I ran into this issue without being able to fix it.
Now i Just found out that our Company CA was configured in /etc/ca-certificates.conf and that the provided file was in DER Format.
After converting it to PEM everything worked as intended.
I have yet to figure out If ca-certificate is even able to ingest certificates in DER format, or if this is an issue on our side. (convert before deploying)
So: No issue here (anymore)
Thank you all, and especially everybody who made Let's encrypt possible!