MKDoc would need some minor changes to add Apache::Filter support, see the documetation:
http://search.cpan.org/search?query=apache::filter
And also this thread on mkdoc-dev:
http://lists.webarch.co.uk/pipermail/mkdoc-dev/2005-April/000280.html
See also the Web Content Compression FAQ:
http://perl.apache.org/docs/tutorials/client/compression/compression.html