Why does a variable size struct not compile in the Arduino IDE?
Flexible array member is a C feature. It does not exist in C++. On top of that, the way you use it to declare and initialize a static struct of flexible size is non-standard even for C. 

However, GNU-C language supports it as an extension. Also, newer versions of GCC (6 and higher) allow this in GNU-C++ code as an extension as well. But GCC 5.4.0 used by Arduino IDE doesn't support this non-standard feature in C++ code.

If you flip through different GCC versions on Godbolt (https://godbolt.org/z/Iul7hD) you'll see that support for this feature has always been present in C code, but for C++ code it first appeared in GCC 6.

This is why you were able to compile it with your standalone g++ compiler (which is apparently a much later version), but were unable to compile it in Arduino IDE.

It means that if you really want this non-standard code to compile in the current version of Arduino IDE, you have to place it into a .c file. Or just specify the array size explicitly.