During the Coverage.py with Ned Batchelder python&testing podcast, Brian and Ned briefly discussed that, if you need to run tests with coverage, it is preferred to run t
I guess I am uniquely qualified to answer this question :)
mwchase and mgilson have it right in their comments: using a plugin means you are depending on that plugin's behavior being correct and understandable. In the name of being helpful, plugins will have their own logic that may have been the best idea when they were written, but the test runner and/or coverage.py may have changed in the meantime. The plugins tend not to be as well-maintained as the other components. If you can avoid them, you have one less thing to think about.
True fact: the reason I added support for .coveragerc configuration files in the first place was because I wanted to add features to coverage.py and didn't want to wait for plugin UIs to be updated to support them.