A command that is not ACKed by architecture cannot be retried. It is the ACK, or lack of one from the Responder, which controls whether a Controller will retry a command. A Broadcast command has no To: Insteon device address value (To: address contains Group number) so no device on the powerline knows to ACK a Broadcast command. Therefore no retry for Broadcast command. This is Insteon in general, not unique to SHN devices.
Linking an Input does not affect the Configuration Register bit but it does override the Broadcast function for that Input. When an Input is linked it no longer generates a Broadcast message for that Input. An input state change for a linked Input will generate a Group ON/OFF command sequence for the Group number that has been assigned to the particular Input.
Unless the Indigo trace is reversing the order of the received bits on the Input status change Broadcast message the bits are in this order from left to right, 6,5,4,3,2,1. The Analog trip points for Analog 2 should be set something well away from the 0/1 values that the trace shows. A floating Analog Input hovers near the 0/1 value and will generate meaningless state change messages. Set the unused Analog 2 trip points to 400 for Off to On and 200 for On to Off. That does not guarantee that a floating Analog input will not generate a state change but those values should keep them to a minimum.
Glad to hear progress is being made. I should receive my new EZIO6I tomorrow. I will verify that it generates Broadcast commands as expected in case you do want to order a firmware upgrade. I don’t think that is necessary to achieve correct Broadcast command generation but will verify on the latest firmware in case you do want to go that way.