This has come up a lot lately. Sage is a “starter” theme, not a theme framework or parent theme. It is designed to be modified, up to and including its core files, to build an effective and efficient custom theme for your site.
If a new feature in a Sage update is absolutely vital to your site, then yes it can be challenging to merge changes from the main repository, but given how bare-bones Sage is, this is a rare occurrence. Sage doesn’t have a ton of theme functionality out of the gate; you add that yourself during development. It’s not like Divi or Genesis where cool new stuff is being added all the time; Sage changes tend to be, like, cleaner error messages when yarn fails, or smarter auto-loading of .scss files during compilation.
I’ve been developing with Sage for years and I’ve never needed to merge changes from the source.