I'm wondering if this is by design or not, however the behaviour seems a lot more like a bug.
If an estate is set to damage but the land parcel is set to safe scripts which check llGetParcelFlags will be told that the land is safe, however avatars and scripts that check llGetRegionFlags will be told the land is damage and will be killed.
Whilst llGetParcelFlags is technically reporting the exact land flags correctly the Estate overrides so surely llGetParcelFlags should be returning that the land is damage, otherwise it is totally useless.