Would there be any mileage in being able to manually say how long you allow the settle to happen in PHD? For example I know that my mount settles very quickly, so anything more than 30s is absolutely going to be cloud of some description (or guiding on a hot pixel). If I could set a time limit to enforce a recovery then that would solve that, without having to draw the distinction between cloud or bad guiding.
In this instance if your mount requires longer to settle then you could put in a time that would be specific to your mount.
That way, there would not have to be any 'is it cloud / isn't it cloud' decision by the software. It would know that after a stipulated period, if the mount doesn't settle then out it into recovery.