Why does the measured back-emf decrease when R is shorted in this circuit?
You are measuring a BEMF which is "influenced" (loaded) by a power supply.

Transpose this scenario into the infinity: if the impedance of the power supply is 0, you cannot measure BEMF because it is dominated by the power supply. If the impedance is infinite, you read only BEMF.

Every situation in the middle is a mix of the two extremities, even without taking in account the magnetic field.