If I power the Arduino MKR WAN 1310 using USB I get 5 V on 5V pin and 3.3 V on VCC pin.
If I power the Arduino MKR WAN 1310 using VIN pin (5 V input voltage) I get 2.9 V on 5V pin and 3.3 V on VCC pin.
Why USB and VIN don't give the same output voltage on 5V pin ?
How can I get 5 V output voltage on the 5V pin using VIN ?
When you power by using USB then you connect 5V to the 5V-line. This line is connected via MOSFET Q2A to the IC BQ24195L, which delivers 3.8V to the linear voltage regulator U6, which delivers the needed 3.3V.
When you power by using VIN, you are connected via the diode Q2B to the IC BQ24195L, which delivers .... (see above). The 5V-line is not powerd, because the MOSFET Q2A is turned off. The gate is at VIN, the source about 0.4V lower ( forward voltage of Schottky diode Q2B).