In the latest beta versions of Channels app on all platforms, we have added a new setting under Manage Sources > Manage Lineup > Stack Duplicates
This now defaults to "By Channel Number", which will combine the same channel across multiple HDHR or TVE tuners, but not across channel number.
The previous behavior is available with the "By Guide Data" option.
With the new default, if you have NBC through a PRIME, OTA/Locast, and TVE, you can see all the entries in the guide separately.