I understand that creating multiple apps through Simulink and running them in parallel is not supported by the UAV Toolbox support package for PX4 as of now.
However, It is a task assigned by my supervisor and I had to report him about this scenario. After hours of fiddling with the source files and simulink, I have come to the conclusion that it might be possible to create and run multiple simulink apps in parallel but it is far too impractical and hectic as even a minor change in simulink design will require a complete reboot of the whole process of creating and running those apps.
To answer your question about using Jetson for all the processing, it is not my choice to do that since I am a student and my supervisor give me tasks to explore and perform.
For those who want to know how I created and ran multiple apps here is a shortened process:
1) First create your first app as usual in Simulink and do the Build only operation.
2) Now goto PX4-Autopilot/src/modules and rename the px4_simulink_app folder to your app name.
3) Then create your next app in Simulink and build again. Do the steps from 1 to 3 for all your apps.
4) Then after final app is created, change all the variable names, function names and module names in the respective app folders in PX4-Autopilot/src/modules folder. (This is the impractical part)
5) After all the modifications, use the (make "your autopilot") command in wsl shell in your PX4-Autopilot directory to build the firmware and get .px4 file.
6) Then upload the .px4 file using your ground control application.