skel/ contains *our* templates for generating a new application. We use [% %] in our templates when we generate a new application. If we used all [% %] or <% %>, the tags for the sample app would get processed out when we generated a new application. So by having two sets of tags, we can use one set generating the app, and leaving the second set intact in the skeleton application.
Good question :) Does my answer make sense?
Jason