Morning Liao,
I've had quite a bit of experience with trying to get an APM agent into Tomcat hosting Atlassian Confluence.
Atlassian Confluence 6.1.0 - CA APM 10.0 Tomcat Agent
With the Tomcat agent, which is a Java agent, it will bind to the class loader, the problem with that is the agent has to be in the right sequence within the boot delegation in order for the agent's dynamic instrumentation to be out of the way of the other bootloaded classes.
Highly suggest you open a support case and reference Case 00768835.
We implemented the same settings for 10.5.2 Tomcat agent and it has been functioning.
Hope this helps,
Billy