I am not 100% sure how the magic works with server, but this sounds like it makes sense. Maybe.
As long as you are not connected to the server in House #1, the app works fine with the HDHR in house #2, with the ATV in House #2.
When you hook up to house #1 is when the issue starts and it sounds like the reason might be because there is no connection from House #2 back to House #1 for the server to feed a 'signal' back to House #2.
At House #2, you are remotely connecting to House #1 via the Channels service and it can feed you the 'signal' for the HDHR that is at House #1, but that HDHR is local to that server, so it has access to serve out live channels from that local HDHR. It is just like it would be if I am outside my house and use the service to access my home's Channels DVR server.
But, that server, at House #1, does not have local access to the HDHR at House #2, so it cannot serve out any channel from House #2's HDHR.
You only had the standalone app working at House #2, before this, and it works with what is local to it, so it works fine with the local HDHR.
Once you connected to the Channels DVR service at House #1, everything has to go through that server and the HDHR at House #2 is not local...or set up with the DVR service at House #1.
So, now I kind of go back to my original line of thought...it sounds like you need a VPN setup between the houses, to allow the HDHR at House #2 to be local to the server at House #1. House #1 server does not need the VPN to serve out the channels, but it needs it to have a local connection to use the House #2 tuners...which is why you are getting the no tuner error...the server cannot see that tuner...even if the app can see it, locally, the server cannot see it locally.
I will let the devs say whether I am way off base, but it makes sense to me.