I think that the issue causing these discrepancies, is how Asobo is displaying the clouds in relation to the METAR. It would appear that Asobo is rendering the clouds from METARs in heights above sea level (MSL), rather than height above ground level (AGL).
See my topic on it here, and please vote so it gets fixed ASAP:
Are cloud bases in new METAR system in AGL or MSL? - Bugs & Issues / Online Services & Activities - Microsoft Flight Simulator Forums