JRiver rips DVDs to a full folder structure, or more correctly just the VIDEO_TS folder, since that is all that contains anything. It doesn't have the option to rip to an ISO. As you say, it relies, in your case, on DVDfab to remove protection and rips the unprotected files.
To rip to ISO using DVDfab Passkey, just insert the DVD into an optical drive and wait for MC to analyse the disc, then right click on the DVDfab icon in the System Tray and select "RIP to Image" ( I think that is what the function is called from memory.) Make sure all your other DVDfab settings are correct, such as location to rip to.
Once complete you can tag the ripped DVD using "Get Movie & TV Info..".