Hi @Maciek ,
1. Yes, for subsystem, you need to mark the subsystem to be treated as atomic and the function packaging option will be enabled in the Code Generation tab, and you can specify there the user defined signature and use that signature in the model header.
2. Yes, for IRQ handler you can take a look in startup_mimxrt1064.c for the IRQ handlers signatures.
I was mentioning that I am looking for another approach and I have another option. The subsystems, in Code generation tab have the below options:

The problem here is how to add a custom section in that drop down. And I came across something that is called custom storage class designer in simulink. (https://www.mathworks.com/help/ecoder/ug/design-custom-storage-classes-and-memory-sections.html)
Default the storage classes and memory sections for a model are loaded from a package called Simulink. Type cscdesigner and will open the below window:

The Simulink package is read only, so you cannot add new memory sections, but you can create your own package. The steps I did:
- duplicate the Simulink dataclass package ( found it here for my matlab instalation c:\Program Files\MATLAB\R2020b\toolbox\simulink\simdemos\dataclasses).
- rename duplicate to +MyDataClasses (find it attached), that I placed it in the toolbox root directory and added to the matlab path)
- in command window, type cscdesigner('MyDataClasses'), and I have my custom package loaded.
- next i could add a new memory section


Then, you need to specify to the model to load the storage classes and memory section from this custom package. This is done from Embedded Coder app, Code Interface, Embedded Coder Dictionary:

I used Manage Package (Refresh to se my custom one in the drop down) - I did an Unload of the Simulink package and then Load of the MyDataClasses.
After doing all the above steps, I could see in the memory section dropdown of the subsystems my added memory section:

The option will be available for any subsystems (including the function call ones).
Hope this helps.
Best regards,
Alexandra