Pollen's current design definitely does not contemplate generating multiple different formats from the same source content.
For example, I'm interested in taking a single set of files and converting it to both HTML and PDF. Not allowed: Pollen requires you to specify a single target format in the filename of the source file.
(Update: Multiple target formats are supported now, see here)
There's a discussion on Github that shows this is something MB is thinking about, though.