I’m trying to figure out how these macros are available in the email templates. Is there any way to create/customize one and use in the template?

The macros available in the email templates are a controlled set, and cannot be customized. Depending on your use case, you could use metadata attributes, e.g. {{ user.user_metadata.foo }}

How does macros like {{application.name}}, {{url}} etc are made available to the email templates?

How does macros like {{application.name}}, {{url}} etc are made available to the email templates?