The JSS has its own built-in CA and also has its own built-in code signing certificate to sign the Configuration Profiles you create in JSS. This all works - as one would expect. However it is possible to upload Configuration Profiles to the JSS that you may have created elsewhere e.g. Apple Configurator or even by hand.
It is possible to sign these using in theory any cert but it clearly makes sense to sign it with the same code signing cert that the JSS is using so that everything is equally trusted.
In fact see this older thread https://www.jamf.com/jamf-nation/discussions/20436/jss-signing-certificate-private-key it raises pretty much the same issue and did not get a successful reply.
I too would like to be able to sign my own custom Configuration Profiles, I can download the JSS Code Signing Cert but I don't get the private key - which is correct. I do however as the admin I have full local access to the JSS server and would therefore be able to access any file and simply need to know which and where it is. I am running JSS 10.4.1 on Ubuntu 16.04.
Whilst I have been able to sign my custom configuration profile using an alternative cert it ends up being shown as Unverified, whereas those signed by the built-in one are of course Verified.
If Jamf regard it as too secret then why not build in a tool to let admins optionally sign uploaded Configuration Profiles?

