Anthony does this patch fill your needs?

Given an @template=subdir/edit it passes :

   subdir/query.edit
   subdir/_generic.edit

to _find() or check(). The tal code then looks for a file with no
extension, .html and .xml.

This modifies roundup/cgi/client.py::selectTemplate() to look for the
last / in the template argument. Then it inserts the class name after
the / or _generic after the /.

If I have a directory html/subdir:

  html/subdir/issue.item.html
  html/subdir/query.edit.html -> ../../../query.edit.html
  html/subdir/user.item.html

http://.../issue?@template=subdir/item uses html/subdir/issue.item.html
http://.../user?@template=subdir/item uses html/subdir/user.item.html

http://.../query?@template=subdir/edit returns an error:

  NoTemplate: No template file exists for templating "query" with
   template "subdir/edit" (neither "subdir/query.edit" nor
   "subdir/_generic.edit")

because html/subdir/query.edit.html is a link to
../../../query.edit.html which falls outside of the html subdirectory.

I think this should work for your template engine as well right?

I am not sure if supporting sub-directories can have some bad
interaction/leakage with the @@file mechanism for accessing files
stored under the html subdir. But I claim there shouldn't be anything
stored there that is not publicly accessible anyway.