MGMorden: I think you are a little underknoledged in the concepts of OS's, or just not thinking clearly. You may have heard the term APIs, or Application Environments? To make a long explanation short, I will use Windows NT as an example. NT has subsystems for many APIs: MS-DOS, 16-bit Windows, and of course 32-bit Windows, but it also has subsystems for OS/2 and POSIX (UNIX). NT runs in the Win32 API, but the NT kernel can look at binary executables and determine which environment it needs to run in and switch control to the appropriate API.
Now, of course BeOS is not nearly as robust as NT, but it would have been very advantageous for them to include more popular APIs.