Android File Transfer cannot see a folder created by app

Maybe "android file transfer" is broken tool?

No.

On Android 3.0+, you need to have your file be indexed by the media scanner before it will be visible over MTP to your Mac. The static scanFile() method on MediaScannerConnection is your best option IMHO.

I just had a similar problem. For Android 6.0.1, simply restarting the device solved the problem.