While conspiracy buffs may be disappointed, this was actually a problem with the BeOS Installer, which is fixed in BeOS Preview Release 2 and later releases.
If you prefer to fix this manually, before you accidentally destroy your BeOS disk, you need to change a hidden setting for the volume to be correct. Then the Mac OS won't look at the drive (or partition) at boot time and offer to blow your BeOS drive away.
To do this, you need to use your hard disk formatter to change the "auto-mount" setting (generally called "auto-mount" or "mount at startup" or something like that) to be OFF (unchecked). If you don't know how to do this, check the users guide for your formatter software for details.