Thanks! I'm starting to think the way the ECU knows which features are installed is by which pin the modules communicate on. For example, on an AWM 1.8T, if ASR is installed, CAN low from the ABS module goes to the instrument cluster and then pin 58 of the ECU. If ASR isn't installed, it goes straight to pin 74 of the exact same ECU. I've seen similar things with other modules. There really isn't much that can be communicated over a couple of un-shielded copper wires running through a car, anyways (except maybe "I exist!"), so this would make sense.
In any case, the ABS CAN low on my A4 definitely doesn't go to the right place right now, and it looks like CAN high will have to change pin as well. I think getting those two wires sorted would help resolve the ABS controller issues once and for all.