When you post-process logs in RTKPost, you need to enter the position of your base station in the Positions → Base Station for the centimeter-level accuracy. There, you can specify the antenna height in the Antenna Type → Delta E/N/U → U.
If the relative accuracy is enough, you can just process with the RINEX Header Position or Average of Single Position options as described in our guide.
Thanks for pointing this out. I was wondering about this too. It seems to me from my understanding that whether you account for antenna height or not, the important thing is to remember what exactly the PPP result is representing in your particular work, the height of the reference mark or the height of the antenna. From what I gather, I think knowing the height of the reference mark is very important if you are going to reoccupy the spot as a base for an RTK survey, since the baseline between base and rover takes into account three dimensions.