You know, I think some of these clear cases have a chemical or composition that can be making these issues arise. Only reason why I say that is due to the amount of people I read with this issue who have said they are "Just using a clear case".
Edit: What also makes me think this is what type of chemicals/coating do they use to keep the case from yellowing, clouding up, etc?
Possible? Maybe. But unlikely from your quote. Because the plastic case surrounds the entire aluminum casing. If you observe the pictures, the chipping/flaking is near the bottom of the grill area only. If the plastic case was causing a reaction from the chemical composition from the anodization, there will be more likely of the phone experiencing chipping/flaking around the other corners or edges as well on the iPhone, not just the grill area.
Furthermore, there have been reports of iPhones experiencing chipping/flaking without the use of a case as well with the two links I posted.
The likeliness of the issue is if the aluminum is not cured at the appropriate temperature or not long enough, flaking/chipping is the end result. Because it's painted, it requires curing before it's finally ready for assembly.
Anecdotally, it seems
some "Product Red" iPhones are experiencing similar issues. Speculation is because the popularity of the color, perhaps the product was "Rushed" during production, which could be the result of the casing issues with chipping.