Hi Peter,
I just tried to create a new metricset named mymetricset under the system module by following the instructions in https://www.elastic.co/guide/en/beats/devguide/current/creating-metricsets.html. I was able to successfully create it without any issues.
One note: the metricsets listed in the modules.d/system.yml file are the ones that are enabled by default (except the ones that are commented out, of course). When you run make update, this file will be reset to it's default state. This default state is determined by the module/system/_meta/config.yml file. If you want your metricset to remain in the modules.d/system.yml file even after running make update, you'll need to add it to the module/system/_meta/config.yml file (and also the module/system/_meta/config.reference.yml file for completeness).
Hope that helps,
Shaunak