What is the advantage of using a motion controller rather than just a PC and BOB?

[Agathon]

a motion controller will generate all the step and direction signals itself in realtime in stead of the pc doing it. the advantage is that a pc might decide to go and check this other thing its doing and take resources away from generating step and direction signals causing problems

Ah right, I get it now. So when my steppers make a noise like they're losing steps (but actually are not) it's down to the computer running other stuff. I noticed it was much worse the other day when I had another bit of control software open.

So, how does a programme like Mach3 or LCNC work with the motion controller? Does Mach3 have a sub-programme to generate the pulses? I suppose that this is bypassed and the G-code sent straight to the motion controller - or is it more complicated?

Oh, and what about ports and pins and limit stops etc?