You technically can profile with both types of data collection agents (ARM agent and JVMPI agent) on the same application at the same time. However, the two agents collect some overlapping data. In the resulting analysis, you might see that a method was called four times, when really it was only called twice, but both agents are reporting the call. Duplicate entries in sequence diagrams could be shown at the host, process, or agent levels (although not anything below the agent level, such as the class or object level).
One example of where profiling with both types of agents at once would work correctly is if you collect performance data with the ARM agent and memory information with the JVMPI agent.