I won't speak from fact , but I don't think a PCM will shut off fuel flow upon deceleration auto or manual. A PCM will keep the fuel system pressurized accordingly. If you accelerate , the demand for more fuel to satisfy the increase in air entering the engine is the same as the adjustment made accordingly for deceleration. Fuel trim is controlled from various means on an electronic sequential F/I system . The idle air control will open as needed upon deceleration to prevent stall as will the injectors will fall back to its pre programmed fuel map at a specific idle speed. The only difference I have ever seen between auto and manual is the actual idle speed , that is with carburetored engines. Electronic injection will maintain idle whether auto or manual.
Decelerating to a stop in gear , clutch out until rpms fall too much is keeping the engine spinning faster due to compression braking while downshifting which may possibly use more fuel due to maintaining idle but there are other factors to consider. Saving gas is the least of your concern. Coasting in neutral is not the best way to treat your transmission . The internal shafts and bearings were meant to work in unison for lubrication purposes . If you select neutral , the main shaft is spinning at road speed but the countershaft is not . A countershaft spins at engine rpm . Manual transmissions mainly lubricate by spinning gears splashing lube to moving parts , there are no oil pumps in manuals. It is best to downshift as you would up shift , rpm and road speed accordingly. If our transmissions were not synchromesh , we would find out fast that we are doing it all wrong. I realize your question was pertains to fuel consumption and not gear shifting , but only an engine at idle will save gas and coasting in neutral in my opinion is penny wise dollar foolish. Holding the clutch in too long has its own faults. Just more excess wear and tear. When I sold my '78 jeep cherokee , the Borg & beck clutch was as strong as I bought the truck . Well over 100,00 mi. and factory original.
I never held the clutch in too long. Off the light , but not waiting at a red. Slowing , I just braked until road speed dictated downshifting . Maybe this is just my way of driving , but I did save the clutch and never had a trans issue. Gas mileage , well , it was a 360 2bbl. and the truck weighed over 4000 lbs. not much you can do about that in stock form .