The htaccess does get rebuilt on every build, but it’s built from a template you can override. That way you can still make changes to the way it works.
The core template file can be found at: /vendor/silverstripe/assets/templates/SilverStripe/Assets/Flysystem/PublicAssetAdapter_HTAccess.ss
You can put a copy of this in your own templates directory, using the same path and make any changes you like. ie (templates/SilverStripe/Assets/Flysystem/PublicAssetAdapter_HTAccess.ss)
Don’t forget to run a dev/build?flush for this to kick in.