It's just different for each OS how you have to deliver files.
With macOS, an APP is always a folder. I don't find that bad, because you can always put all the files that belong to the app in it.
It is only macOS specific and difficult for the compiler to distinguish what should or should not be in the APP folder. In addition, the compiler has to adjust the target path for resources especially for macOS. This is more of a guess.
So it is better to work with your own tools in the IDE. That is what it is intended for.