Yes, C++ interop is difficult and filled with traps. Cold hard rules are that you must use the exact same compiler version with the exact same compiler settings to build the modules and ensure that they share the exact same CRT and standard C++ libraries. Breaking those rules tend to get you C++ classes that don't have the same layout on either end of the divide and trouble with memory management when one module allocates an object using a different allocator from the module that deletes the object. Problems that lead to very hard to diagnose runtime failure when code uses the wrong offset to access a class member and leaks memory or corrupts the heap.
Node.js avoids these problems by first of all not exporting anything. NODE_SET_METHOD() doesn't do what you think it does, it simply adds a symbol to the Javascript engine's symbol table, along with a function pointer that's called when the function is called in script. Furthermore, it is an open source project so building everything with the same compiler and runtime library isn't a problem.