For the sake of clarity, I assume that the only change is the part footprint on the PCB and we should be retrofitting 100nF caps on rev 3 boards as well in the existing footprints?
In Rev 4 C21 and C22 are replaced by a smaller part footprint, for the 0.1uF (instead of 10uF). They were moved a bit to make space also for the optional C54. But there is no change to the electrical circuit as such. On Rev 3, it is equivalent to replacing 10uF capacitors C21 and C22 with 0.1uF.?