Where is the apache2 filebeat module configured?
After looking a bit further, I found it in the sample called filebeat.full.yml


So I added this section to the filebeat.yml
Restarted filebeat 


After running at 100% CPU for minute, Kibana is now immediately showing the results. That was easier than I expected.

#==========================  Modules configuration ============================
filebeat.modules:

#------------------------------- Apache2 Module ------------------------------
- module: apache2
  # Access logs
  access:
    #enabled: true

    # Set custom paths for the log files. If left empty,
    # Filebeat will choose the paths depending on your OS.
    var.paths: ["MY-CUSTOM-PATH"]