We are also using OneAgent to monitor the Apache/Java/WebSphere etc. I was curious to know the benefits of using this extension on top of the existing PaaS monitoring.
You should always use the most applicable OS as that is what determines which commands are executed and what the expected command output is. A common cause for missing metrics is the relevant commands not being found/on the path.
If you haven't, check the troubleshooting guide: https://www.dynatrace.com/hub/detail/remote-linux-monitoring/#troubleshooting
The other possibility is something is unexpected in the output of some commands and that would need to be identified and handled. A support case is best in these situations so that the output can be communicated.
The logs should tell pretty clearly which scenario it is.