I think the key is the line about "metadata".Even though a file does NOT have a double extension, it can still have metadata at the top of the file which needs to be scanned and read. The double extension really just tells docpad to convert the file from one format and output it as another. If I create a straight html file in the document folder I can still include the metadata header in the form:
---
tags: ['tag1','tag2','tag3']
title: 'Some title'
---
When the file is copied to the out directory, this metadata will be removed. If I do the same thing to a html file in the files directory, the file will be copied to the out directory with the metadata header intact. So, the answer to your question is that even though your file has a single extension and is not "rendered" as such, it still needs to be opened and processed.
The point you make, however, is a good one. Keeping images and documents together. I can see a good argument for excluding certain file extensions (like image files) from being processed. Or perhaps, only including certain file extensions.