Damir, you open too many mostly unrelated topics. Too much for me to process. Just some quick notes:
When you delete songs, only the audio files attached to these songs are deleted. Same thing happens when you restore a backup. Only audio files, attached to songs are deleted before restoring the backup. When you then refresh the song list, it will pick up all leftover audio files and add them to your library. I guess that's why you see these duplicates.
ST3 uses the title tag as the default song title. It will only use the file name when there is no song title.
To go to the ST3 folder, open settings and scroll down. You will find a shortcut at the bottom of the settings page.
To store audio region settings, export a song through the export feature as a .stsa file.