SharePoint 2016 Application pool issues with new SCOM 2016 Agent

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Recently I discovered that the  SCOM 2016 agent crashes SharePoint 2016 sites.
Error: Server Error in ‘/’ Application Runtime error

Tasks I performed trying to correct the issue;

1. Changed Central Admin site web.config and turned Legacy mode off. (This worked as expected but... Microsoft doesn't support this scenario)
2017-08-15 14_13_45-NuStar Energy LP Servers  - TXLPHQSSPAPP16 - Royal TS
2. Installed Update Rollup 3 for SCOM 2016 but not luck as they still have the issue.
3.  Uninstalled the SCOM 2016 agent and everything came back up as expected but no monitoring which is not acceptable for a critical system like this.

Workaround/Temporary Resolution

Re-installed the SCOM 2016 agent via command line utilizing the following command msiexec.exe /i momagent.msi NOAPM=1 which disables/removes the SCOM APM module which breaks SharePoint (.Net/IIS modules)
APM service removed.
After removing the APM module everything worked as expected.

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