Power good state when Pull up voltage and Input Voltage is different

PWRGD will accurately indicate the fault modes of the LT3072 as long as BIAS is high and it should not matter if EN or IN are high or low - see the Power Good section in the datasheet.  I will double check that in the lab as soon as I can and update my post if necessary.  Your 1k pullups for the PWRGDs seem too small, especially for PWRGD2 that is pulled up to 5V.  Can you target 100uA or 200uA for the PWRGD currents, since those currents are more typical for the LT3073 according to the datasheet?    

PWRGD will accurately indicate the fault modes of the LT3072 as long as BIAS is high and it should not matter if EN or IN are high or low - see the Power Good section in the datasheet.  I will double check that in the lab as soon as I can and update my post if necessary.  Your 1k pullups for the PWRGDs seem too small, especially for PWRGD2 that is pulled up to 5V.  Can you target 100uA or 200uA for the PWRGD currents, since those currents are more typical for the LT3073 according to the datasheet?    

Also, you don't have sufficient CBIAS according to the datasheet, and your IMON resistors will cause current limit at 1A.