Both my 6.9s didn't have the factory water separators, and as far as I know, came that way.
Rock
Maybe Ford committed the sin of undocumented mid-year alterations on the last 87s to roll out and you just happened to get two such examples of it.
The 78 Dodge van I had, it had mostly different 1979 wire colors when I had to do some wiring repairs. They must have run out of 78 harnesses and started using 79 ones. It had round headlights so it couldn't have been a 79 model, since 79 started using rectangular ones with different fenders for the wraparound turn signals.