Yes, the Tomcat they've bundled is pretty standard, the only stuff they've really changed is to embed their application in it.
I've not tried SCOM myself, but I know it supports Tomcat, and when I've hooked up other tools, I've never needed to do anything other than follow the standard "talk to a generic Tomcat" documents for them.
I've dabbled with Monitorix, Nagios, Zabbix and a few others. Depends on the client though. Jconsole is handy if you don't need a monitoring/scanning system as well.
My input is quite light-weight though - most of the meetings about monitoring go "how to we integrate with Jira/Confluence", and the answer "well, it's a standard Tomcat" has been enough to get the monitoring teams on the case for me.
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