You can adjust parameters in your model while it runs (i.e. MATLAB will generate C code from your Simulink model, send it to the BeagleBone, build the code on the BeagleBone, then run the code on the BeagleBone.I'm not sure if that helps and I'm not a Linux user 'yet' so I can't answer any specific questions. I think you can install some versions of Linux onto a Windows box and just boot into Windows when you need to, my friend does this on his Mac box. Actually, that's about all I need Windows for otherwise I would've converted to Linux already.The Matlab runtime environment on linux is 2013a and in windows is 2013b.
This software was developed on Sun/Unix and is also supported for DEC/Ultrix and VAX/VMS as a system for data management, display and analysis system for observational.