It ended up being an issue with damaged pads under the CPU. As it turns out, 15V → 5V conversion is done by the chip marked DC0 and VSYS → 5V by MAX8969. Due to a lack of proper connection with the SOC, the EN signal for DC0 IC wasn’t present which was the cause of my problems with this switch.
In the picture below I marked good readings for this area along with my findings about this circuit. Check whether you have an EN signal for DC0 (should be 1.8V when present). You can also check the EN point in diode mode and if you have a connection issue like I did it will measure around 0.7V.
One important thing is that 5V output will come up only when the switch is fully booted up and you connect up a joycon or the fan is spinning - which makes it hard to measure this area for voltages.
