yeah it comes down to the remap really, get on the blower and ask em how they sort the idle. i was assuming the pipe in the pic was for the isv, but it might be for the breather system or even just there to blank off the unused isv pipe on the 2e inlet boot!
kr isv controller should work fine with a 2e isv, or if not a kr or abf one will be fine. the aav might be a bit too simplistic for this but its something that you can try dead easy as all you need to do is plumb it in and give it 12v, see how well it copes. the best way though is as danny says get it sorted as part of the remap

megasquirt ecu doesn't use any kind of idle control, so i see no reason why a good AGG map would be a problem. main thing is do they have the ability to do it, since the agg ecu is different internally. in fact the chip may be soldered direct to the board and not removable, but im not sure exactly which mk3 ecus are like this