Best way to alter Drupal entity?

One of the Drupal entities is Aggregator which comes with a defined set of how to save these entities using DrupalCoreEntitySqlSqlContentEntityStorage

Would you agree with me that while I can alter the MySQL table that it would be ultimately self-defeating since it would be overwritten in the next Drupal core update? And better to alter it in a custom module?

With the new paradigm in Drupal 8, I don’t know enough to say this is the best path? thx, sam

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