During simulations, almost all blocks in this package directly feedthrough signals and do nothing. For example, the IMU block has inputs, which are fed to the output during simulations, so running in continuous should be no problem. I shall test to see again tomorrow when I am back at my lab.
You never want to run a simulation model in a micro controller for several reasons:
1) The purpose of the simulation model is so that you could test your controller before using it on your physical platform. When deployed, your vehicle's actual dynamic response replaces your simulation model.
2) The ATMEGA2560 chip is very slow and can only run in discrete time. You will never get a good sample rate if you decide to run a complex simulation model on it.
So the advice is to test your controller in MATLAB/SIMULINK using the dynamic model, then upload your controller to the APM2.5 for validation and deployment.