HeXEn installs both config files, because at the point it sets up the files it doesn't know which BIOS you are going to choose. One is on C:\, the other on E:\, because that's how the two BIOS writers decided to set up their BIOSes. If you'd spent the time looking instead of ranting you'd have found them both in under ten seconds. You might also have worked out that editing an X2 config file would have no impact on an iND BIOS.........
The sound issue has nothing to do with your BIOS. It's your Xbox hardware, or your cable, or your TV.
There are BIOSes on HeXEn for all versions of Xbox. If your Xbox boots then you have picked the correct BIOS.
The FTP directory issue happens occasionally. I have no idea what causes it (and before you start ranting again it isn't a HeXEn issue, it can happen at any time). My recollection is that rebuilding the disk usually sorts it out.