Given your description, you have Internet delivered through Ethernet from the ONT. So, the ONT does not use MoCA to communicate with G3100, and the ONT will not be a part of the MoCA network. Nonetheless, this does not imply the ONT coax cable can be disconnected from your MoCA network.
I think there was some confusion. FNA stands for Fios Network Adapter, which is your ECB5240M. I asked you to connect only the G3100 coax with ECB5240M coax. I has not asked you to test the MoCA connection between the G3100 and the ONT. There will be no link and should not be a link.
Regarding the service charge, if the technician finds the issue originates from your configuration error instead of product defects, you are most likely to be charged.