With the Distributed Per-Test Coverage feature, Clover has the ability to record per-test coverage from tests that are running in separate test JVMs, which may be co-sited or distributed around a network. This allows you to roll together results from unit and functional tests, from JVMs running different test frameworks, possibly in remote locations, yet resulting in a single unified view of your project's per-test code coverage.
Measuring per-test coverage allows you to run Clover's new Test Optimization on your functional tests. A battery of functional tests (being generally more time-consuming than unit tests) strongly benefits from the ability to run only the tests on code which has changed.