[magic_quotes]

> people will just run the Linux version

Don't worry, there are more than enough stumbling blocks in Linux emulation to ensure it would never be as convenient as native applications. For example, if you pass LD_LIBRARY_PATH with FreeBSD libraries to the Linux program it will predictably blow up in your face. Now, imagine running a shell script which calls FreeBSD and Linux executables.

Linuxulator is really a method of last resort and it always requires special care for each individual application.

[trasz]

This one is trivially solved using jail or chroot. Otherwise, there’s the path translation mechanism (/compat/linux) specifically for this purpose.

[magic_quotes]

Nah, not quite the same. Jail makes it easy to avoid calling FreeBSD binaries from the Linux process by accident. If you must mix-and-match commands, jail is exactly of zero help.