When I start playing, the BGM of the main menu doesn't stop, it stays in-game and I know it's not meant to do that because it overlaps with the actual in-game BGM.

I tried turning the BGM off and even restarted my PC but nothing works... it's annoying and ruins the setting for me.

I’m having the same issue. 

I FIGURED IT OUT!! When I hovered over the eden’s garden icon on my taskbar there were two tabs and the music was coming from one of them so I just x’d out of it. that’s probably the issue you’re having.