You are right that the features are slightly different. The Xoom2/XYBoard has a built-in IR blaster, while Dijit on the Galaxy S2 and other devices work with the Griffin Beacon. The Beacon hardware can function as a learning remote, which means that it has a sensor to learn buttons from your existing remote controls. The built-in hardware on the Xoom 2 does not support learning and uses a bit of a different process to get the remote codes for your devices.
If you're having trouble controlling one of your devices, I'd suggest you post the brand and model number here and let us know what isn't working.
-- Zach Lipton, Dijit Software Engineer