The only reason I can think that this wouldn't work is because of tolerances. Depending on how tight the tolerances are on the drop-in liner, it may not fit after a spray-in liner is installed. Remember, the spray-in liner coats the inside of the bed from 1/8 to 1/4 inches thick, changing the inside dimensions. So the drop-in may not fit after that.
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1999 Lariat SuperCab Flareside, Amazon Green with Silver trim, 5.4L, 4x2, 4 wheel disc/ABS, 3.55 limited slip, towing package, fog lamps, sliding rear window, captains chairs, keyless entry with alarm, spray-on bed liner, bug guard, and K&N.
http://www.csc.calpoly.edu/~bfriesen/truck.html