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The ECU doesn't care what sort of equipment is installed on the bike. All it cares about is air/fuel ratios. It measures the air/fuel ratios with the O2 sensor(s) in the exhaust and will simply keep on correcting the fueling table until it achieves the ratios it wants. So if the bike you install the system on has pods and a 2-into-1 then the ECU will tune to the correct air/fuel ratios for that setup.
The only concern I might have would be that Ecotrons sends the ECU to you with a "basic" tune installed in it. If this basic tune is for a stock intake and exhaust setup it would be too lean for a bike with pods and a 2-into-1 setup. Of course, the ECU would immediately begin correcting it, but there would be a period of too-lean running.
Maybe it would be best if Ecotrons would ask you ahead of time about your intake and exhaust configuration and send you an ECU configured with a basic tune that corresponds to that setup.
(I know that part of the appeal of the Ecotrons kit is that it's pretty much plug-and-play on a stock EX-250, which explains why it comes with two O2 sensors and the ability to maintain two separate fueling tables, one for each cylinder. But because I'm only speaking from my do-it-yourself fuel injection perspective (Microsquirt rather than Ecotrons), I haven't worked with the Ecotrons kit and I don't know what you would have to change/reconfigure anything for a 2-into-1 exhaust which usually means you need only one O2 sensor.)
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