BeerSmith applies your thermal expansion to all volumes which are measured 'hot'. So if you have the default 4% thermal expansion, this 4% is applied to your strike volume, pre-boil volume, and the estimated post boil volume. The program does NOT scale the volume based upon temperature. Given this, for a thermal expansion of 4% your most accurate measurements for the above mentioned points to correspond to the program estimates would be taken right at boiling.
Cold volumes which are estimated and measured are your volume into the fermenter and trub and chiller loss.