The filter will be engaged if you select rec-709F in any of the preset which allow you to select custom colour profiles, so definitely all the user modes (user1, user2, etc or whatever you have renamed them to).Awesome. Thanks.
To use 709F one should be in THX mode? Or is there another way to engage the filter?
It's the colour profile that triggers the filter, not the user mode. THX calls the filter because it uses a color profiles defined as using the filter. I don't think it allows to call a custom colour profile.
In other words, when you create the custom color profile in the JVC software, if you specify the filter during the creation of the filter, the filter will be called whenever that colour profile is in use, so during the Autocal as well. So all my "F" colour profiles engage the filter, all my "NF" colour profiles don't.