@mbartosh You were right to be skeptical. I was disappointed to find that the matching of usage data is purely by process name alone.
I ran the following Relevance query on the machine showing Oracle Java Runtime Environment usage:
q: image paths of instances of application usage summaries "java.exe"
A: C:\IBM\TDI\V7.2\jvm\jre\bin\java.exe
A: C:\IBM\SMP\maximo\tools\java\jre\bin\java.exe
Both of these javas are from IBM, obviously. I then queried BigFix for the Total number of Runs:
q: total run count of application usage summaries "java.exe"
A: 192
This matches the reporting in BFI, as seen in the screenshot below. Clearly, the path of the executable is not taken into account when matching usage data from BigFix with usage signatures in BFI.

This is what the documentation has to say on the subject.
The usage data is first collected when the BigFix client is installed on an endpoint, and an application usage statistics is enabled. The statistics are displayed on the Metering Data report. When the processes are matched against usage signatures from the software catalog, or custom usage signatures, the statistics are available on the Software Classification panel.
You will have better results using an analysis in BigFix to capture the paths of the running java.exe processes.