But the idea of ePod is to always convert it to POD, and produce nice well formated POD.

There is not a big difference between "can produce POD" (and HTML) and "always produces POD". So why a "But"?

What I think interesting on OODoc is the use of templates to generate the HTML. How they work?

Just like CGI templates: have a constant template, which indicates where dynamic data must be filled in. You can best look at the examples included in the distribution. For HTML you may need a lot of templates, but for POD it is very very simple.

In my experience, POD (being a visual markup language) does not contain sufficient information to create good HTML. The resulting HTML can be much nicer. See for instance the Mail::Box docs. For the author, it still looks like POD...