The answer is quite simple - your calculations deal with the average rate taking into account all additive and subtractive processes and in terms of rock, not sediment,
One lesser point is that sedimentary rock is compressed, so that it occupies less volume than the equivalent loose sediment.
But more importantly there have been times where there was erosion - quite considerable erosion. The base of the Grand Canyon - including the Vishnu Schist represents the roots of mountains that were raised - and destroyed by erosion. The boundary between these rocks and the higher, later rocks is known as the "Great Unconformity"
See the picture at the bottom of
this page
There are more - if less impressive - examples of erosion between strata further up the canyon.