I am responsible for the basic cloud flags. You are correct that the 1.6/2.25 large and small scale histogram tests and the IR histogram tests are not included in the summary flag. These tests were not considered to be working well and therefore it was decided to remove them from the summary flag until they are fixed, but all the individual cloud test results are still there. There is an auxiliary file (PCP) which indicates which of the basic cloud tests is combined to produce the summary cloud.
The large scale 1.6/2.25 tests have since been improved and are now included in later releases of the data (products processed with processor baseline 2. 10, IPF version 6.09). The small scale hist tests are still being worked on. These operate in regions flagged as 'sun glint' and so the cloud flagging is not optimal here yet.
Therefore, the summary cloud flag should be used to avoid cloudy data, but it can still be useful to check each separate cloud test and combine them for your own purposes.