Now you are confusing a number of different things. Einstein used a free-falling sealed box to derive the equivalence principle. This does not imply that any f

Now you are confusing a number of different things. Einstein used a free-falling sealed box to derive the equivalence principle. This does not imply that any free-falling system is a sealed box. Thinking about clocks makes absolutely no sense without having a way of comparing them. In your example, the clock in the center of the earth will run slower than the one falling from the tower due to gravitational time dilation. Note that Einstein's "light clock" thought experiments do not capture this effect, since it stems from General Relativity, not Special Relativity.