You should be able to do this through the api by setting the course_navigation[default] of the external tool to enabled. See the link and specific settings below:
https://canvas.instructure.com/doc/api/external_tools.html#method.external_tools.update (scroll up a bit to the create call to see the options you can set)
course_navigation[default] | | string | If set to “disabled” the tool will not appear in the course navigation until a teacher explicitly enables it. If set to “enabled” the tool will appear in the course navigation without requiring a teacher to explicitly enable it. defaults to “enabled” Allowed values:disabled, enabled |
I assume this relates to your question about Zoom. In the configuration XML it is set to default to disabled (<lticm:options name="course_navigation"> <lticm:property name="default">disabled</lticm:property>).
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