I work in a ClearCase shop and CC does a good job of integrating the team's work though our code review process prevents me from using it to track my daily changes. Creating an hg repository on top of my CC view works really well. I can track my changes and easily make backups on the file server, produce diffs for people etc.
This is all well and good until I move to a new CC view and have to leave my history behind. I would love to be able to ?pull? my previous history in and have everything that's different in the new view show up as the latest change set.
We use Git inside a ClearCase static view, for pretty much the same reason you described - finer grained control.
In CC, when we start working on a newer (labelled) release and the config spec changes appropriately, Git picks that up as a regular changeset.
The magic works precicely because Git knows nothing about config specs, and CC knows nothing about the .git directory. When the config spec changes, it reloads whatever files have changed but doesn't touch the .git dir, so Git still sees the repo.
I don't have any experience with Mercurial, but I just fired it up then and added a few dirs and files, and it appears that it works the same way.