I used it for a while with CP, maybe a year ago. There weren’t any problems back then and it was OK. I just ended up deciding that I didn’t really need it as I have so few plugins, the ones I use I trust and auto-update was easier.
Edit. I don’t recall any warnings or issues with sites being CP.
Actually looking here: "Must Have" Plugins List
They are aware of CP and did test it quite a while ago. You can’t use it to update CP core files.