And just like that, it's solved. I figured out the mystery of the Equipped Device Table.
The answer was in some obscure piece of System V Release 3 source code. The 3B2 system board has a 16-bit register called the Control and Status Register (CSR). In the CSR is a bit called named TIMEO that I never figured out.
It turns out that I just wasn't reading the disassembled ROM code closely enough. The exception handler checks this status bit whenever it catches a processor exception while filling the EDT. If the bit is set, it skips the device.
So what is TIMEO? It's the System Bus Timeout flag, according to the SVR3 source code.
The correct behavior, then, if nothing is listening at an I/O card's address is to set an External Memory Exception, plus set this bit in the CSR. Once I implemented that in my simulator, the EDT started working exactly the same as it does on my real 3B2/310. Success!