The ClearPass server certificate and the Onboard CA are two different things. If you are talking about the self-signed certificate under Administration --> Certificates --> Server Certificates this is what is used for HTTPS and EAP termination.
The CA for OnBoarding is located under the Guest side of things. Depending on your version, it may appear under OnBoard + WorkSpace --> Initial Setup --> Certifiate Authorities. The level may vary for versions without 6.2 that don't have WorkSpace.
This is the Certificate Authority which signs and issues certificates to OnBoard devices. However, if you are pushing out certificate trusts through your Network Settings (for the above EAP certificate), you may need to find a way to get that on the devices.
To verify, check one of your OnBoard certificates to see what CA issued it and what the expiration time is.