I am on Sharepoint 2013, we migrated from Sharepoint 2010. I have custom popup page which has the following CSS declaration:
<head runat="server"> <SharePoint:CssLink runat="server"/> <SharePoint:Theme runat="server"/> <title></title> </head>
In the 2010 version I can see that the stylesheets are loaded properly, but when I inspect with Chrome the popup on Sharepoint 2013, it doesn't even put the css tag on the page.
Consider that the page should work out of the box on any Sharepoint platform, so that's why we don't specify the CSS version.