Does anyone know how to do that?As this won't work if you have several files with the same name in a project (just in different directories) it's very unlikely that this will be implemented. However, you can adopt the AutoSave plugin yourself and just add a "../save_folder" in front of the save command.
if(::wxFileExists(filename) && ::wxCopyFile(filename, temp))
One idea would be implementing some form of file name mangling based on variables,You can also just leave it as it is (which won't conflict) and use a file manager that allows to hide file names with specific extensions. That's how I do it.