If the waiver was denied by USNA, it's likely the end of the road. DD (not you) may be able to obtain additional information regarding her medical situation from either her admissions counselor or the medical staff person at USNA. I wouldn't start with "Why didn't I get a waiver" as much as, "I see that my waiver was denied. Is there anything that I can do to potentially change that determination for this year or next year?" Such things could include a stronger package overall (probably not helpful since she was obviously a strong candidate or they wouldn't consider her for a waiver) or a change in medical condition (probably not likely given the reported condition). But worth asking.
I'm not aware of any appeal process for a denial of a medical waiver. I suppose if there were a substantial change in the condition, one could submit that information, but usually DODMERB / USNA requests the information they deem sufficient to make a determination.
DODMERB doesn't grant or deny waivers -- they only qualify or DQ. If they DQ'ed and USNA has not "ruled" on the waiver, there is still hope.
As to why some candidates are granted waivers and others are not . . . no one here can answer that question. Could be the medical condition itself (as we frequently say, no two individuals are the same). Could be a limit on mids who can commission with that condition (e.g., colorblindness). Finally, USNA can't bring in too many mids who aren't medically qualified to commission in the unrestricted line. So, if eczema is limiting in that respect (I don't know whether it is), that could play a factor.
