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Solved it.

So it is absolutely fine to have a flat plugin structure (as I did for this simple test). My issue was that my controller had the line: goal_check_loader_("cc_nav", "nav2_core::GoalChecker") when it should be goal_check_loader_("nav2_core", "nav2_core::GoalChecker").

I was taking inspiration from the dbw controller plugin in which the SimpleGoalChecker is loaded from dwb_core, so I thought I needed my package in the first argument. The dwb goal_checker_loader instantiation works because the SimpleGoalChecker in dwb_plugins is exported into dwb_core from a separate package: pluginlib_export_plugin_description_file(dwb_core plugins.xml). In my case all my plugins are exported into nav2_core.