The Harem ticket was separate I think because it is the largest building in the palace and the most striking. The building that most people show interest in visiting. We visited it in winter and it was very crowded. I guess in summer it will be much more crowded. And it is common in some countries that these museums/palaces have separate tickets for some of the most popular attractions.
!PIZZA
To be crowded in winter and summer, that tells a lot about that place. If I were to visit the palace, that would probably the first one I'll check :D