To derive time dilation you need two stationary clocks and one moving clock. In the rest frame the two time readings (emission and reception) happen at the same point, but there is a second clock, that has been synchronized with the first one, that is needed to compare with the moving clock at the later time. We say that the measurements are made at the same point in the moving frame, but at different points in the rest frame.
So even though it seems like emission and reception are at the same point in the rest frame, a supposedly simpler situation, there had to have been a previous measurement involving two separated points. When you derive time dilation using light clocks, you usually look at the light traveling in one moving clock and one stationary clock, but you are allowed to do this because the two separated stationary clocks have already been synchronized.
Einstein makes this this statement in his 1905 paper: "We assume that this definition of synchronism is free from contradictions ..." If he can, I can.