The only difference in the default similarity options between Toolbox v.3.2. and all versions after is about including or not the whole aromatic ring as a single characteristic when the similarity is calculated (see Fig. 1 below).
Figure 1
In Toolbox v.3.2 the whole aromatic ring is taken as a single characteristic, while in the next Toolbox versions each of the atoms in the aromatic ring is counted as an individual feature.
Figure 2