Hi Moon Wolf, this is not a cubasis only problem none of the other music apps I have seems able to properly identify inputs available. I use a cheap little usb audio interface which has mic,line and digital inputs. With one exception none of the apps recognise the inputs available and all default to the mic input.
The exception is…Garageband. It correctly identifies all the inputs and allows selection of left,right and stereo line inputs,mic input or digital. There is a trick that selecting the input in Garageband and then closing Garageband and loading up another app keeps the input selected in Garageband. So if you have Garageband might be worth a go.
Not one of the other app developers have addressed this either nor do they seem to show any intent to do so either.
I think there is something in IOS that apple know the others dont.
Hope this may help