The main reason is that for leadership votes (and all parties use a ranked ballot for their leadership), we are electing an individual, while for general elections, we are electing a representative body. 
The reason this is important is that ranked ballots are bias towards the center because people on the left rank their votes left to right and those on the right rank them right to left, so they end up meeting in the center.  
So when electing an individual, this is good because it prevents candidates from being too extreme, and we are more likely to elect a more consensus candidate, then an extreme one. 
However, when we are electing a parliament, it is supposed to be representative of the support that a party has from the public, and a reflection of the various views that the public hold, if we elect parliament this way then the people who hold views that are too far away from the center will not be reflected in parliament.