I can't speak for GitHub but I've worked on multiple nav headers for large SaaS products and they can be ridiculously heavy weight to render given they appear on every page. They tend to be a dumping ground for features, many of which require their own permissions checks, feature flag checks, etc. it's not unusual to have to perform hierarchical permissions checks. They also tend to contain contextual info about the current nav state and dynamic information about navigable states.

A lot of this can be cached but it's easy to see why moving from one repo to another will invalidate most or all permission checks and feature flag checks.