Thanks for sending me a Scarlett 4-4 to test with! This is a new unit, and I opened it and connected it to an iPad Pro 10.5" (2017) via a powered USB hub. I didn't connect it to a Mac first or make any attempt to change the default settings in the unit.
In BandHelper, I have Play First Two Recordings Together and Multi-Route Audio turned on, with Recording 1 L/R mapped to Scarlett USB 1-2 and Recording 2 L/R mapped to Scarlett USB 3-4, just like you showed in your screen shot.
When I clicked the recording button for a song with two recordings attached, recording 1 played through the line out 1-2 jacks and recording 2 played through the line out 3-4 jacks. So this seems to be working as expected without changing any settings. (Only recording 2 played through the Scarlett headphone jack, but I think that's how it is designed to work, based on the graphics in the Focusrite Control app.)
Next, I connected the Scarlett to my Mac via a direct USB cable and installed the Focusrite Control Mac app so I could look at the default settings and compare them to yours. When I first opened the Focusrite Control app, I got an alert about being in Quick Start mode and clicked OK to restart (screen shot attached). Then the settings appeared, with Monitor Outputs 1-2 and Line Outputs 3-4 both set to "Custom Mix" and the custom mix set to Software Playback 1-2 for both (screen shot attached). Without changing any settings, I then reconnected the Scarlett to the iPad and tried again with the same iPad settings, and then only recording 1 played through all outputs. That matches what I would expect the new settings to do.
I reconnected to my Mac and, leaving both pairs of outputs on Custom Mix, changed the Software Playback of outputs 3-4 to Playback 3-4, then reconnected to the iPad and then only recording 2 played through all outputs. It turns out the custom mix is shared by both pairs of outputs, so changing the custom mix for Outputs 3-4 to Playback 3-4 also changed the custom mix for Outputs 1-2 to Playback 3-4. So if you need to use a custom mix, you can only use it for one pair of outputs.
Then I reconnected to my Mac and changed Monitor Outputs 1-2 to Playback 1-2 and Line Outputs 3-4 to Playback 3-4 and Loopback to Analogue 1-2, just like in your screen shot, then reconnected to the iPad and everything played as expected again (screen shot attached).
So we've learned a few things:
- Settings changed in the Mac app are indeed saved and carry over to iPad use
- The jacks labeled Line Outputs 1-2 on the Scarlett hardware are labeled Monitor Outputs 1-2 in the Focusrite Control app
- The headphone jack on the Scarlett hardware only plays whatever is routed to Outputs 3-4 (I think)
- The out-of-the-box default settings will do what we want
- The updated settings after running the Focusrite Control app for the first time will not do what we want
- At that point, changing the custom mix for outputs 3-4 will not do what we want
- Changing the outputs for 1-2 and 3-4 to Playback 1-2 and 3-4 will do what we want
What I don't know is how we seem to have ended up at the same settings, but mine works as expected and yours doesn't. After having done various tests, can you make sure your BandHelper and Focusrite settings match what I've described here?
Also, you included a screen shot of a "Bundles" window, but I don't see that in the Focusrite Control app. Is that from a different app?