High end pcb repair equipment question...

I was looking at some of the very expensive test equipment used to
troubleshoot circuit boards and it seems that they all use the Huntron type
of testing. Injecting an AC signal and then viewing the results on a screen
and then comparing that to a working board. Equipment made by Polar, ABI,
QMAX, and it seems most of the people who make industrial test stuff where
you place the board under a bed of nails type test fixture. My questions
is, is this the only method that us used to troubleshoot complex pcbs? If
so is there a good web site that covers the details of how this is done? I
guess there are many variations on this method but none of them are perfect?
are they? Even with one of these systems and a known working board can you
still be unsure of what is exactly wrong with the board? And... Are there
any other radically different types of systems used to troubleshoot complex
circuit boards and how might they work?
Thanks for the info
Russ