I don't know enough about programming to follow that easily, but I'm trying. :)
It seems to mean that the main Lua executable has this extra code that makes writing functions easy, whereas it might be desirable to use system calls to bypass that for speed or size reduction in finished code. If this is right, it makes sense in a way, but if Lua contains the stuff I used in the manual, and it is a core part of Lua, it seems that this might be taking reductionism to the point where it seems odd to go to such lengths to undercut Lua after taking the time to build/use it. Or is this basically a way to bypass the usual layers that seperate the user's program from the hardware?