To clarify a few things from my research and testing:
EKA enabled/disabled - disables the need for the EKA - say it's gone flat with the battery connected, then you'd need the EKA more than likely when the power is restored. Turning EKA should stop this from being required. The only time it will screw you is if the EKA is turned OFF and KEYCODE LOCKOUT comes up on the dash - it implies the vehicle is in an alarm lockout stage, and needs the EKA - which if it's off, it won't accept.
If you have a V36 or later BECM, the 'Disarm' section in the Nanocom will still allow you to put your EKA number in and disarm from the lockout (in most cases - sometimes even then the BECM will not do it, and will need sending away to someone like myself to have the lockouts reset using the faultmate/BECM CPU module.
That being said - I've had a few test BECMs on the bench and I've never been able to get one with the EKA disabled into a state where I can't recover it with the key - I've tried multiple different scenarios, including simulating breaking into the vehicle whilst it's alarmed, and with the EKA off, it was simple to reset every time.
Immobiliser enabled/disabled - this disables the passive part of the immobiliser system. The bit where it will re-immobilise the vehicle are 30 odd seconds, with the idea being that when the vehicle detects a key being put back in the ignition it pulses the coil around the key barrel, which then induces a small current in a coil in the key fob, which triggers it to send an unlock code - which then re-mobilises the vehicle and will allow starting. If this is ON and your key fob stops working, then you will need the EKA every time it automatically immobilises again to be able to cancel it and start the vehicle, which is one of the reasons most people turn it off - it creates a headache in my opinion, especially if your fob is iffy, or you've only got one. Turning the passive immobiliser OFF disabled this automatic immobiilising, but the vehicle WILL still immobilise when it is locked and alarmed with the key in the door.it also turns OFF the coil around the ignition (the BECM doesn't pulse it when it detects the key in the ignition), which also then disabled the 'friendly sync' where an out of sync fob will automatically resync when you put it in the ignition. The only way of syncing the fob, with passive immobilisation disabled is to do it with the key in the door.
Alarm enabled/disabled - pretty self explanatory - with it disabled it won't trigger any of the alarm responses if it detects the vehicle has been broken into. I've not seen any other detrimental effects having it switched off on the test units I've played with, but would leave it switched on out of habit myself. I believe that the security LED on the dash which usually flashes when the alarm is armed, will still flash as a deterrent (at least on a number of the boards I've tested - might be software/firmware related) when the vehicle is locked, but the alarm isn't ACTUALLY armed.
Key Warning... I believe this is just a gonging sound from the instrument pack sounder which gets pretty annoying pretty fast, and sounds if the vehicle detects the key is in the ignition, and the drivers door is open. Removing the key from the ignition shuts it up. Most vehicles I've looked at have it disabled by default, and I think it was more NAS spec that had it enabled.
Immobilisation strategy. Regarding the link between the BECM and the engine ECU and Diesel/Petrol differences.... Early EDC vehicles appeared to just ground the immobiliser line between the BECM and engine ECU and that was the immobiliser trigger, nothing complex at all. Though these were swapped out pretty early on for the 'Late EDC' version (it's not a 99MY change as you'd expect to line up with the GEMS/Thor changeover on the petrol vehicles - it was actually in '96/'97 from memory). Late EDC has an immobiliser code which is hard coded in the engine ECU, and this code then is programmed into the BECM. The BECM then transmits this code to the engine ECU constantly, in pulses every 144ms? Quite rapidly anyway. When the BECM is disarms/non immobilised and the key is turned to position 2, it transmits the code constantly until the ignition is switched back off (or to Pos I)
GEMS petrol has a code in the BECM which it transmits to the engine ECU. If the 2 become out of sync, then instead of programming a code back into the BECM, you tell the GEMS ECU to enter security learning mode and it will then take the next code sent to it by the BECM as it's immobiliser code, and stores it - so instead of changing it at the BECM end, it's done at the engine ECU end. When you turn the key to POS II, BECM transmits the code to the engine ecu where it checks it, and then if it's valid, then engine ECU illuminates the Check Engine Light as a response that it's happy. When the BECM sees this trigger, it stops sending the immobiliser code altogether, and then will allow the starter motor to operate. The Thor petrol is pretty much the same as the Late EDC - code is hard written into the engine ECU, and then programmed into the BECM to match. It's then constantly transmitted when the ignition is on.
Both the EDC and Thor Petrol models DON'T respond back to the BECM to say that they are happy with the code. GEMS won't crank until the CEL has been switched on (confirmation of valid code from engine ECU), and thus WON'T crank or show CEL if out of sync. The EDC and Thor petrol will always still crank - as the BECM has no idea if the code is valid or not, as no feedback from the ECU. So it's programmed to always allow the starter to run, and then the actual starting is decided by the engine ECU - if code is valid, then injectors/spark etc are allowed. If code isn't valid, then these are disabled. On a Diesel, I believe it will shut off the fuel stop solenoid or something in the FIP to prevent fuelling if the code doesn't match.
Hope that explains a bit more in detail how the various systems/options work for those who are interested.
Marty