Using: 2 each (hdhomerun3_atsc 20150406) and EyeTV 3.6.9
Back when I added a second HDHR3 to our system we could still get OTA via cable. I connected it to such and was able to configure EyeTV using one device on us-bcast the other on us-cable. Each HDHR3 got its own channel list in EyeTV, making channel assignment possible.
HDHomerun also has a channelmap called kr-bcast.(Korea) (The designation of channelmaps: us-bcast/us-cable/kr-bcast is HDHomerun specific.) I have selected kr-bcast in HDHomerun_gui.app and was able to tune a local station. If there is a way to get EyeTV to use kr-bcast for one device, I'm hoping EyeTV will repeat the desired behavior. I have no idea if the alternate channelmap will disrupt Guide population for that device. If so, the "Assign EPG Channel" may solve it.
In searching the SiliconDust forums and HDHomeRun Development Guide, there is a [/lineup/location] parameter that goes back to 2011. Seems it is not implemented for the older devices/firmware. No idea if EyeTV uses it.