First thing. Forget the misnomer that inputs of an operational amplifier always have the same voltage. This assumption does not work when the thing gets saturated, is used as a comparator and on other instances.
A simple and effective way to look at an opamp is: If the voltage at the non inverting input is higher then the voltage at the inverting input, then the output goes to a higher voltage. If the voltage ata the non-inverting input is lower then the other input, then the output goes to a lower voltage. That is all there is. Often a balance is reached (and both inputs will have the same voltage) but not always.
For the analysis.
1. Assume Q1 is "off" at startup.
2. Non inverting input is at Vref.
3. Because Q1 is "off", non-inverting input is also at zero volt.
4. Non inverting input has highest voltage, and thus output of the opamp will rise (slew rate limited).
5. Base voltage of Q1 will also rise, as a result emitter of Q1 follows the base voltage (minus 600mV).
6. Vin = emitter voltage and will also rise.
7. Inverting input of opamp will also rise, (With fixed ratio because of R1 and R2).
8. This continues until the voltages at the input of the opamp are the same.
9. If the output of the opamp would rise further, then the non-inverting voltage would be higher then the inverting input.
10. ... And that would result in the output voltage getting lower again.
11. Thus the circuit stabilizes itself.