I want to understand plugin implementation of custom posts / taxonomies / metaboxes

Let’s start by looking at the Action Reference page in Codex: Actions Run During a Typical Request.

When a page is loaded on the front or back end, WordPress goes through the load process- loading its own code, loading plugins, the theme, calling each action in sequence.

You can see in the second and third actions where it registers the native types- post, page, etc..

The environment is built this way for each request- a post type exists for the life of a request, and disappears if the plugin that registered it is deactivated.

However, the actual data- your posts, taxonomy terms, custom field values- are all safely stored in the database. If you were to register the post type with another plugin using the same name, your post type would appear and be usable again.

So, in short, as long as a plugin adheres to the WordPress API, you aren’t in danger of losing that data

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