If you want to add variables for a specific domain then you would add those variables to a dialplan that is now called domain-variables. It used to just be called variables however when I added a global variables dialplan it made sense to rename it to domain-variables. These are channel variables for a call.
Advanced -> Variables is primarily used with SIP profiles. Used to be applied to all calls but that changed at some point. The SIP profile interface is simple enough that advanced variables isn't that useful anymore unless making a variable that are likely to be changed. So we will likely rely less on Advanced -> Variables in the future. Considering adding it as a category in default settings.
Default Settings has many variables for provisioning for the theme and for various features in FusionPBX and these settings don't make sense to be channel variables for calls.