That is a very good description of the problem with extended commands. To further complicate the matter, the extended portion is not sent twice as the "standard" portion of the command is.
In addition to the ACT repeaters, the XTB-II does recognize extended commands, and will not transmit them in the basic repeater mode. It does provide the option to receive them and pass them on to the automation controller if that is capable of recognizing them. It does transmit any extended commands received from the automation controller.
One thing I am trying to grapple with is how best to deal with extended commands in the enhanced repeater unit. As you point out in your tutorial, it is not possible to begin the repeat in sync with the second half of the standard portion of the message. However, delaying the repeat until the entire extended message has completed will consume almost an additional second of powerline time, and will obviously step on any message that was tailgating the original extended message. It is possible to monitor the powerline, and abort transmission if a collision is recognized. However, that will delay transmission of the extended command even further, and it is possible that the out-of-sequence transmission will induce other unforeseen problems. Any inputs regarding this complex issue are welcome.
Jeff