Hi Jonas,
As you correctly point out, in this case the molecular calculations are not affected by BSSE as you are extracting a single molecule (i.e. with no neighbors).
The calculation that is affected by BSSE is the one on the crystal, where each molecule within the molecular crystal could potentially "benefit" from the basis functions of the neighboring molecules if its own basis is not complete. So we use MOLEBSSE for this, to make sure we compare apples with apples (i.e. the energy of a molecule in the crystal that has access to the basis functions from neighboring molecules, with the energy of an isolated molecule that also has access to the same neighboring basis functions).
Hope this helps clarifying things a little,