The proper way to wire these cars with ISIS and inReserve is to have only the stuff that requires constant power (ECU memory and stereo memory) wired direct to the battery. That's it. The way most engine harnesses are wired, you run your starter cable direct from the battery to the starter, and the engine harness picks up it's power from there.....so no wiring changes are required to provide the ecu with constant power.
Yes, while the ISIS is powered up, it constantly monitors voltage and kicks the whole system off at 12.2 volts. At that point, the ISIS system is dead. It is no longer monitoring voltage. The ONLY things at that point that have power to them is the ecu and stereo memory wire. I do not recommend allowing ISIS to kick the inReserve off. Wire up the inReserve so it is either triggered by ISIS OR by a manual momentary push button (comes with the inReserve kit). If you allow ISIS to kick it off every time, it will deep-cycle your battery over time and ruin it. When you leave the car, hit the momentary button and the whole car is dead with the exception of the stereo and ecu memory. Your car can sit for months on end like that. I see the ISIS inReserve voltage monitoring as nothing more than a back-up in the event you forget to manually kick the inReserve off. When you want to drive the car, simply hit the momentary push button again and the whole car powers up with a full 12.6v battery.
With this other battery cut-off with the remote, it is constantly drawing power on it's own, to receive the signal from the remote. You're wiring up a component that has it's own built-in battery drain (ironically) to prevent battery drain?