In most cases that is how it works with dev => staging => production. You don’t actually make changes to the productions site, in some cases in some environments it is impossible to make changes directly to the code on the live site.
Quite frankly, I find it a PITA as well, but I do work on some sites that are on systems that require this.
1) You perform updates and coding changes on the dev site
2) You pull code changes to the staging site from the dev site and db from the live to test
3) Finally you pull code changes to the live site.
However, you could simply install a plugin like https://wordpress.org/plugins/download-plugins-dashboard/ and just download them from ACF from the dev site and upload it to the other two sites. For several versions of WP it now detects that you are uploading a plugin that is already installed and prompts you replace it with the new upload.
