I found this thread concerning the question how to inbound external files (such as style.css) by refering them relativly:
http://social.msdn.microsoft.com/Forums/en-US/sharepointdevelopment/thread/9bc131c3-db38-46b2-992a-abdcf2dac9b0/
I tried to apply this approach to set the favicon (or other images such as: SiteLogoImage, etc.) also relativly in the HTML Masterpage.
Therefore I tried following links:
<!--SPM:<asp:Literal runat="server" Text="<link rel='shortcut icon' href='" />--><!--SPM:<asp:Literal runat="server" Text="<% $SPUrl:~sitecollection/Style Library/Themable/client/images/favicon.ico %>"/>-->
<!--SPM:<asp:Literal runat="server" Text="' type='image/vnd.microsoft.icon' />" />-->
<!--SPM:<link rel="shortcut icon" href="<% $SPUrl:~sitecollection/Style LibraryThemable/client/images/favicon.ico %>"/>-->
<!--SPM:<SharePoint:SPShortcutIcon runat="server" IconUrl="<% $SPUrl:~sitecollection/Style Library/Themable/client/images/favicon.ico %>"/>
But anything works :/
What do you think?