You can choose which TiVo to use, but you can't select which Stream it uses to transocde. It just automatically picks the first one it finds on your network. I don't think they ever intended people to have multiple Streams.
Note even though the Roamio Plus/Pro have an internal Stream it's still treated just like the external one. So even if the show is on that same TiVo it's still streamed across an internal network switch before being transcoded and sent out to the iPad. The Stream inside a Plus/Pro can be used by any Roamio or Premiere on your network, not just itself.
Developer for VideoReDo