Hello,
Custom certificate on WebADM and WAProxy are used for HTTPS 443 access (Admin and webApps accesses).
Web services like OpenOTP use a certificate issued by WebADM internal PKI which are webadm.crt and webadm.key located in /opt/webadm/pki/ folder. This certificate must NEVER be replaced by a certificate issued by another CA, else you will encounter issues.
It is useless to do that because it do not increase the security. If you put a public trusted certificate here, then all certificates issued by that public CA could be presented to OpenOTP API and access will be allowed based on CA trust, which is finally less secure than using WebADM internal PKI because you have no control on certificate issued by public CAs.
If you would use certificate generated by another/your internal PKI for e.g, then you have to reconfigure WebADM as a subordinate of your internal CA and re-issue all certificates of all products already deployed where a certificate has been issued by WebADM PKI (Radiusd, LDProxy, WAProxy, WebADM, Spankey...) Else you will have issues. So I clearly discourage you to go that way as it doesn't involve any security improvement and there is lot of impacts behind.
Here is a documentation to configure WebADM as a subordinate CA:
The last WebADM versions prompt you now in the setup script, the possibility to configure WebADM as a Sub-CA :
Setup WebADM as a Standalone CA (1) or Subordinate CA (2) ([1]/2)?
To configure WebADM as a Subordinate CA, you need to copy your Sub-CA certificate and key as PEM format in /opt/webadm/pki/ca/ca.crt and /opt/webadm/pki/ca/ca.key
Regards