I am NOT a part of the Shopify team but it will probably always remain that way, at least for the foreseeable future.
When you update your theme, it does transfer over some basic customization's, but if you have custom code in the theme files, often it does not.
One reason for this is with every updated version of a Shopify theme there are new features and code, which would cause your custom content to not function or display properly even if they were inserted into the files. That is why the code needs to be manually added to the updated themes files and it isn't done automatically.
I know it can be tedious to have to do this with each update, but it probably will not change anytime soon.