Note that the Simulink Target - actually programs the board - and runs on the board. So when you hit play in Simulink normal mode - you didn't initiate that workflow (and just get the color bars). that is a means to test prior to running on board. Although with External Mode - you also can monitor execution in Simulink - you can see that in either of the examples below.
Separately - it isn't clear which workflow you actually want/prefer. you may want Simulink to run in simulation mode and get Rpi inputs/outputs while MATLAB/Simulink is running (similar to the MATLAB Support Package for RPi). That is not included in either support package.
It would be helpful for us to understand if you do want to have the ability to perform input/output device from Simulink with Rpi (as you do with MATLAB) - without programming algorithms on board. If you can help us understand your usecase for this feature - we can consider future improvements.