Mutt,
Skipping back a few posts, yes, I'm well familiar with the Boeing Instantaneous gradient at commencement of 2nd segment, and other manufacturers cuch as McD stipulating Field pressure as the data entry point.
John_T and I were / are products of the Australian system where there was often conflict between the airworthiness requirements and operational rules were oft at loggerheads on this issue. The operational folk took the viewpoint that using a lower reference Pressure Height "consumed" a portion of the Gross Vs Net Delta as 2nd segment continued and was thus unacceptable. Consequently, reputable operators like Ansett and TAA / Australian took the more conservative approach. (I'm sure that QANTAS probably went the same way).
In practice, there's only a minor penalty, and in 99% of cases can be avoided. For a MAA of, say, 500 ft and an end of 1st Segment height of 100 ft, use of mean 2nd segment PH means using 300 ft AFL, a small penalty. This equates to approximately 10hPa conservatism, and for a B777 amounts to approximately a 2500 Kg penalty. As 99% of Takeoffs are with reduced thrust (ATM or Flex) this penalty may be recovered by a couple of degrees of Assumed Temperature reduction. In the other 1% of cases, there's a penalty, but the good folks at airworthiness at the regulatory authority won't compromise upon any degradation of a climb gradient required for obstacle clearance.
What use is the WAT limit? For my 2c worth, it offers a minimum standard of performance for the aircraft, irrespective of Runway and Obstacle factors which are another issue. Of course, we do know that there are people "out there" who go flying with WAT as the only limit regardless of Runway / Obstacle computations, but there's always a few rotten eggs in the basket.
Regards,
Old Smokey