Like you said, need for table prefix change is very rare or one could think of it at the time of installation. However it is needed in some migrations and that is why WordPress developers have thought about it and include that as an option in wp-config.php
e.g. Scenario
You already have a site with table prefix wp_. Later date you want to download and improve the site locally and upload that to the same host to get feedback from your visitors.
Since the original tables are with wp_ your new version table names should start with a different prefix to reside in same database without colliding with your existing site data. So you may choose site1_ as your table prefix. Then you can import the new tables in to same host db while having exiting site and new site files in two different folders.
