Indeed, during step 2 algorithm of the software computes all the possible points and later applies filters so that only reliable point would remain. In such a way a densified point cloud that provides an accurate background for distance, surface and volume measurements is generated.
However, please keep in mind that the quality, level of noise in the cloud depends on the various parameters such as type of terrain, quality of images, overlap, point cloud processing options.
For more information about point cloud processing options: https://support.pix4d.com/hc/en-us/articles/202557799
Additionally, it is possible to apply filtering and smoothing in step 3 which are used to generate the DSM and orthomosaic. These options are related to the Step 3: https://support.pix4d.com/hc/en-us/articles/202557769