The need for the second filter , has to do with the filtration capacity , of both filters .
The first filter in the system ( with the water separator ) will probably have a 20 micron filtration capacity . Consider this a filter for taking out the lump sized , particulates in the fuel.
The final filter , will have a filtration level of 3 micron , so it only has to deal with particulates , in the 3 to 20 range.
If the system only had the 3 micron filter , to deal with all the particulates , it could plug up very quickly , and require very frequent changing.
Remember the , fuel system on these engines , use excess fuel to lubricate and cool the high pressure injection pump , and even at WOT will return as much as 70% of the fuel; supplied to the engine ; back to the tank . By the time you use a tank of fuel all the fuel will have been through the filters about 7 times ; that's why these filters can plug up so quickly.
99DSDP 3884, Freightliner, XC, CAT 3126B, 300 HP /ALLISON 3060
2000 Caravan toad, Remco & Blue Ox.