How can I share external functions between App Designer app and other apps (C#)

I have been struggling to share some external matlab functions so that they can be accessed by both a C# application and a standalone App Designer app. The overall structure that I need is this;

This works so long as I run the matlab app inside Matlab. However I need to release it as a standalone tool for others, without Matlab, to use. The Matlab app will call the external functions if I add their location to the path. However, this doesn't work if I compile the application and then install it as a standalone app. What I think happens is this ...

The compiler creates compiled versions of the external functions and they get installed - hidden away in the AppData directory and not easily found! The Matlab application now talks to those versions even if the path of the shared external functions is added in the application. As a result any changes made to the external functions are not used by the standalone app - unless it is recompiled to keep the 'ghost' functions up to date.

Does anybody have any suggestions on how this can be done?