"... they actually don't start retracting until after the train starts moving and bumps them slightly. "
Really? Bumping a stationary item? That doesn't sound safe. I have seen yellow signs with black lettering, at the platform ends, that state "SLOW UNTIL GAP FILLER SIGNAL CLEARS" The signal has a red lamp, and a lighted white section with the abbreviation for gap-filler, "GF". When the red lamp is extinguished, the train can move at normal speed. I believe that the initial slow forward motion of the train is detected by a track circuit, (similar to the practice of "keying by" a stop signal) which then retracts the gap filler. When the gap filler is fully retracted, the signal clears.
On another note, I believe that there are gap-filler platforms at the west end of the shuttle between Grand Central and Times Square. Unlike the other ones at South Ferry and 14th Street, which are the intersecting grid types, the ones at Times Square are more like the ones you have built. They are solid and slide under the fixed platform.