What's the difference between Lojack embedded in the system BIOS or low-level and Lojack just installed on an otherwise normal computer?
Lojack software just installed on a computer can only hide itself as well as any other software program. The right tools can find and disable it.
Integrated into the hardware it is much harder to disable and eradicate.
Lojack works, though, on the principle that the odds of a theif taking a lojack-enabled system versus a non-lojack enabled system are relatively low. So most thieves will probably not think or take time to check for the existance of this tool.
You would probably benefit from reading the Absolute Software Lojack technical document. It's not very technical and goes into some detail regarding how the system works. From this you'll be able to see how the system may be gotten around.