As the originator of the "always" - that was obviously based on a fully functioning system with the 3-wire being the target. Clearly if the engine is knackered or the pendant isn't rigged then the "target" will change. AIUI the default setting on the Fresnel is for touchdown just aft of 3 wire (2' or so if memory serves), which goes to show the precision involved. As Orca says you can adjust the alignment to vary the touchdown point if required by circumstance (defective system, recovery case).
Three wire systems are going to be the norm (four Mk7 engines - one for the barrier) from CVN76 onwards, but all CVN prior to that still have the 4 wire system. Charles de Gaulle is a three wire system as well I think. You just change the position relative to the rounddown / fantail based on glideslope and desired hook - ramp clearance.