If it’s using multi channel association, Both the trigger and the target are encoded in the byte structure for the wrapper around the basic set command. See the link above with all the details.
Now when the association group is triggered, the device should send one instance of the relevant command(s) (e.g. a BASIC_SET) that is not encapsulated, plus another two instances of the command(s), each encapsulated within a MultiChannelCmdEncap() wrapper to the appropriate endpoint destination.
But you have a point: I have no idea how you get to the wrapper in a smartthings context. Or if you even can.
As far as what the Tweaker does or doesn’t do under the current V3 app, I don’t know for sure, you would need to ask in that thread. But I know there are still people using it with the new app.