we have a solution with a Module for static files. In elements.xml we would add each file like this
<Module Name="Files" Url="Style Library" RootWebOnly="True">
<File Path="Files\css\design.css" Url="css/design.css" Type="GhostableInLibrary" />
</Module>
The problem is that when updating the file the E-Tag is not always updated, for instance if we ask for If-None-Match: "{C51DBB4F-B5EE-4826-9960-864EF6FA967C},1" we get 304 NOT MODIFIED, because this is what the old file had, but the new file responds with E-Tag: "{C51DBB4F-B5EE-4826-9960-864EF6FA967C},1" which is the same as the old.
Update:
We do not use CssRegistration