The WGS84 altitude in HomeLocation does not refer to the common altitude (usually MSL : Mean Sea Level) of a location but takes in account others parameters like the Geoid separation:
Altitude (WGS84) = Height (MSL) + Geoid Separation
Look at the altitude displayed in the Attitude tab > Settings
After a clear, this value should be updated automatically using a reliable GPS position and Geoid separation coming from GPS.
Next you should use this altitude value as reference for your HomeLocation/POI settings.