Nah as far as I know you don't have to register it for the outer templates. You just pre-register variables when you need to use the variable inside of that template. You don't need to go through it's hierarchy registering it for each parent template.
For example I had to pre-register my custom header template for the 'header' template. Then any custom variables I wanted to use inside my custom template I just registered directly for that. I didn't have to register them for the 'header' template too.
The thing I did find though which seemed senseless to me is that if you register your variables for the same custom template in more than one place for example I registered the code for an avatar in one plugin and the rest of my variables in another plugin. Then I found that I needed to re-register those variables. i.e. I found that because I had called the create/render lines for my template again it had unregistered the variables I had already registered. Now that certainly confused me lol.
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