There is a real "danger" of a bad result if the flat areas are cut separately from the 3D toolpaths.
I've seen it a lot over the years from photos posted of completed projects...what happens is you get a halo effect around the 3D model. It's nearly impossible to avoid because it's nearly impossible to set exactly same z-zero between an End Mill and a Ball Nose. (Not to mention material movement alters the Z Zero point anyway.)
So why do people do it? To save time, that's all. Unfortunately, the outcome is often compromised. "Halos" around the 3D models are unattractive to me.