In that sense, only 3 IPL teams are included because the 4th one has to go through qualification. Actually, IPL is the most popular league and hence it's 3 teams. Pakistan's league is the least popular and that's why even it's winner has to make through the qualification to play the champions league.
The IPL was conceptualized by the Indians in partnership and with support from the Australian and South African boards. Hence the Aussies and Safricans have two automatic spots each. Hence the IPL having 3 automatic spots and one qualifier.
Ironically enough the inaugural tournament was won by an Australian team with no IPL team making the semi final. We ask why? Basically after this competition the IPL teams had the best T20 players on their teams, when it came to the CLT20 in the following tournaments the players obviously stayed with their IPL teams over the their domestic teams since the Indian league offered them more money.
If we had the foreign players opting out of the IPL, all the Indian sides would also have to go through the qualifiers as the Paks and Kiwis!