I have a multi store setup on the localhost, one store on the main domain and the other on a sub-domain. As soon as I apply a custom style in default, it never gets applied to the 2nd store i.e. the sub-domain one. Even if I change the scope to the the store on the sub-domain, then to the style never gets applied. This is a bug in the Magento system, I guess.
As I have to manually go the the directory and and edit the files in the "\pub\media\mgs\css\2" then only the css is changed for the sub-domain, if that is the scenario, why even these is an option to apply a custom style to the other multiple stores.