It seems likes I am limited by the shoutem builder to having a default Main Navigation, whereby all of the other screens are wrapped by it. Is it possible for me to create a landing page where my users can sign in, and then segue to the Main Navigation? How would I achieve this?
The shoutem.auth (Users) extension does something you're asking for. It displays a screen before any shortcuts (i.e. navigation items) are displayed. It achieves this through the use of a middleware which is implemented throughout the entire Shoutem app, visible in the @shoutem/core package.
You could use a similar pattern to achieve your landing/onboarding page extension.