A few users have complained about automatic updates of the plugin overwriting their custom code changes. There is nothing in Seamless Donations that makes it different from any other plugin in terms of automatic updates.
Most likely, if you’re experiencing automatic plugin updates, you’re either using a plugin or a service that is providing those updates to you. Personally, I use a service and have it automatically update all the plugins I use on this site and my other sites, because I’d rather take a possible functionality hit than leave a security whole open because I might not have gotten to doing updates in time.
That said, if you’re extending core functionality, you’re likely to experience overwriting and you should definitely make backups. It’s in the roadmap of Seamless Donations to add better extensibility features in the future.