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If I were a Triumph engineer, I would order the igniters without the unneeded drivers for the coils that are not there, saving a bit of cash. This would mean that you couldn't interchange 360 and 270 units. Beyond that, the timing curves and the rev limits as well for the 790, 865 carburetted and 865 injected engines are completely different so as to match with the valve timing changes.
Now, considering that, even with increased rev limits the 270 degree engine just won't run as fast as the 360, both coils must be firing at the same time and the lack of core saturation at high speed is killing the spark. They are probably using separate ignitor outputs because the unit is too small to contain drivers large enough to manage 2 coils.
Note that Gill say these units automatically detect whether they are running on 12 or 24 volts. This makes me suspect that at least some of the problems experienced with these bikes are caused by high voltage in the electrical system. Suppose that the voltage to the igniter reaches the switchover threshold, maybe because of a poor ground somewhere in the system. It would switch to 24 volt mode, probably reset at the same time and the engine misfires. Then the voltage drops and it switches back with another reset and misfire.
The igniter has an RS232 programming port. This normally takes 9 connector pins, but you can get by with 6 or less with a minimum of 3 if you are running in an open loop async mode. The igniter programming is password protected so you would need to do some hacking to get in or buy an unprogrammed unit from Gill to play with. At any rate, you would need an address chart before you could know how to go about reprogramming it.
I think the third timing lug was put there in readiness for the fuel injection system.
I was just thinking the exact same thing! 
Howbeit when He, the Spirit of truth, is come; He will guide you in all truth:
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