Flying my P4P on the weekend, I noted my machine was losing altitude in a hover. I would estimate the rate was one metre per ten seconds. So after reviewing a number of my flights where I have landed exactly at the takeoff point, I have seen that in a large proportion of the flights, the altitude recorded on my iPad suggests I have landed up to six metres underground.

Is this a normal issue or something that can be readily rectified. While I wouldn't normally worry about this, it obviously can impact on RTH. (Sadly, I am without the drone at present as it has been returned via the retailer due to transmission issues.)

Given that you have returned it, I wouldn't worry about it since it is quite likely you will receive a different aircraft back!

Might be sensible to raise the issue with DJI so that they can take a look at it while it is in for repair anyway.

It is not unusual to have errors in barometric altitude, a change it temperature will affect air pressure and thus the height reading so you should always leave a big margin for error when using the barometric altitude, and when setting RTH altitude.
  
It shouldn't have the same error every flight though, if it consistently looses 6m per flight over many flights then there is a problem.  If it is always only 6m then I wouldn't worry though, that is not a big error for a barometer.