I setup a config file using the example in the online documentation, but some of the settings aren't being used.
In particular, the imports/show-imports setting. I tried setting the "imports" to yes as shown in the example config file. The generated epydoc-log shows that though imports is set to yes, the show_imports is still no, and no imports appear. Adding --show-imports to the command-line then makes the imports appear. (I tried setting show-imports to yes in the config file, but then it complained about an unknown config.)
Also, the inheritance setting doesn't seem to have any effect. I set it to "grouped", but it still comes out in a format that looks like listed. It also may not be being read from the config file, though I'm less sure since I can't tell the difference between the different settings.
Great beta though, I love the new features!