Another update: I have just finished with update 3.6.5 and there will be a change regarding this issue.
You will be able to select an internal sample rate of either 44.1k or 48k which Stage Traxx will use. Switching sample rates will require a restart of the app. So it will not be possible to adapt to the sample rate of an audio interface while the app is running. But it will allow you to run the app in the sample rate that your multitrack files are using.
You will still need to stick to one sample rate for all your multitrack files. There is no way around this. But in my tests I had no issues with audio interfaces running a different sample rate as long as multitrack files and internal sample rates match.
When adding a multitrack file with a different sample rate, you will now see a warning message.
Version 3.6.5 will be available in the next few days.