In Khadas VIM3 thermal_zone0 ans thermal_zone1 represents temprature for (A53 CPU and A73 CPU) or ( CPU and GPU )

cat /sys/class/thermal/thermal_zone1/temp

If it can only measure the temperature of CPU , how to get the temp for GPU and NPU

there are only 2 thermal capturing points on the SoC, thermal_zone0 and thermal_zone1
you can take average of them for overall temperature of the SoC (all components inside the A311D SoC)