You should be skeptical of anyone who says that there is a single “right” way. The right way depends on the situation. Using the CPT infrastructure has a number of notable benefits:
You get the Dashboard UI for free
You automatically take advantage of WP’s caching, including any persistent cache plugins that the installation may be using
You automatically get goodies like post revisions
You get access to the WP_Query class, which means that, in theory, you don’t have to write any (or at least not much) likely-to-be-buggy-and-vulnerable-and-inefficient SQL
If you’re planning on distributing the plugin or opening it up for open-source development, you may find that developers are more comfortable using custom post types and the associated API functions than your own custom stuff
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