I'm going to rephrase your question into what I think you're trying to ask.

You are currently using XML and XSLT to create HTML and PDF versions of your XML file. You want to know if you can get rid of the XSLT process and just use Template Toolkit to turn your XML in PDF and HTML?

For the HTML output, sure you can do that. It should be fairly simple.

For the PDF output that'd be a little hard. TT Templates are more form-like, where PDF syntax is more of a language (IIRC similar to PS). But you could use one of the many utilities to convert the HTML to PDF. Though, that may not look the way you want.