Even though Coder doesn't need to check out a full Drupal install, I'm finding that I keep running into issues with the hard-coded expectation that a full install exists. Putting the coder checkouts into /checkout/sites/default/modules/modulename would help alleviate some of these issues.

In addition, it would allow for tests which have multiple modules included in the test arguments (not that I can think of a situation which would require this ...).