So the version with the resistor at the ground side has a slight advantage, as it is not that much effected by the supply voltage. The difference is not because the resistor is at the emitter, but because the resistor is towards ground.
I think it could be the other way around.
First let's think of voltages as the difference between two points (this makes things a bit less confusing). There is the voltage across the resistor V_R and the voltage across the phototransistor V_PT. Let's assume we can measure both independently and choose either as the output measurement.
It doesn't matter which way around you arrange the two components (R on top or R on bottom) you will have the same current travelling through both the R and PT. This means that V_R will be the same regardless of arrangement. This means that V_PT will be the same regardless of arrangement. The question comes down to whether or not V_PT or V_R is a better output in terms of rejecting noise from the main power supply, not which one is on top/bottom.
I vote V_PT being better, because if it acts anything like a diode then it will have a reasonably constantly voltage drop even if the main voltage rail changes a bit.
(If this is true then putting the PT at the bottom might make more sense, as measuring voltages in reference to ground is the norm and might (?) make opamp choice easier)