Not sure what happened but after playing around with REW(room equalizer wizard) with my audio interface using ASIO drivers with the Audyssey DM-A409 calibration mic. I was able to confirm that the mic was 100% working. I connected it again to my Denon AVR-X550BT receiver and ran another setup. Lo and behold the mic was able to finish the speaker calibration without any issues.
So far after the calibration I measured the speaker distances and everything seems that the values seems to closely match up.
Not really sure what happened, but I've been trying this for days but it was not working at all. Now the Audyssey DM-A409 mice is now working.