clock skew vs clock latency

Let reinstate my view. case 1 tells TimeQuest that data is offset from its clock launch edge by ([expr $DATA_delay - 0.5 + $Tco_ADC]).

case2 tells TimeQuest that data is offset from its clock launch edge by ([expr $DATA_delay + $Tco_ADC]). Although you specify clock latency but that is applied to a clock called something else and I don't know how this new clock name will be related to data clock (virtual or otherwise).

I personally wouldn't care about using latency. Moreover different results may also occur if you realise that timequest does not target theoretical optimum point but it targets passing timing and stops there and so your verdict is best gauged if there is pass/fail difference.