Like I said, can't say how well it works as I haven't got two remotes so haven't distinguished between them as such. To answer your question simply, it seems like yes, you can distinguish between remotes. Then, on your Apple TV > Settings > General > Remotes, you can pair the remaining remotes. The issue is, until you do that, it states under the option for disabling the IP receiver 'This computer will work with any available remote.'. You can then pair which remote you want to your iMac. If you click that, it will tell you how to pair the remote. This is because Ferd II must have one paired.
No more being elbow-deep in the sofa cushions looking for your lost remote Jailbreaking your Apple TV is not required, because AIR Remote uses default infrared codes. It uses the infrared blaster to replace or extend your Apple TV remote in an smart way. As can be seen in the image, it says 'Unpair' under the option 'Disable remote control IR receiver'. AIR Remote lets you control your Apple TV with your Android phone. I don't have two remotes, so can't fully confirm if it works properly or not, but there is a 'pair' function.
