I was in (a little slow-going) contact with the support and they confirmed this as a bug that will be fixed in a future release. There’s no quick fix for this it seems.
If you’re looking to reverse-engineer Core functionality, just look it up in the source code: https://github.com/WordPress/WordPress/blob/master/wp-admin/options-general.php#L229
wp_timezone_choice() generates the select options. You’ll likely need to create a custom way to parse this into your ACF select though.
As for saving the field, the original option value should do. That’s what the WP options page does at least.
