I think the interpretation of the images may be in error. From reading the stuff I can find, the very first bunch of pulses (just a block under the first column) are for remotely setting up the speed lights. The first case is to setup A/B/C for TTL mode. The 2nd case would be setting up A/C for TTL and B to manual.
For each TTL group, the master first send a group select command, then send the pre-flash (low) command. If the camera sees a weak reflected light, it will ask for a 2nd pre-flash with higher intensity.If the return from first pre-flash is good, it will skip the 2nd pre-flash. The reason for this is to save the energy on the remote flash.
The camera calculates (no calculation needed for manual group) the amount of flash needed for each group. It transmit the amount data for all groups in a batch (the block from master under Column All). After a pre-determined time, all groups fire the flash using the amount data received.