Why, on carrier landings, does the Flight Path Marker (FPM) seem to be placed near to the end of the runway?
The short answer is that it is because the carrier is moving toward the point that the FPM is indicating; where the ship and aircraft will converge at the moment of landing.

In reviewing my answer to the other question linked in the comments, it struck me that some clarification might be needed to distinguish between landing visually, or by reference to ship based ILS, versus flying a HUD equipped aircraft.  In the first two cases, (visual or ILS) the frame of reference is the ship itself.  Whether the ship is stationary with 30 knots or natural wind across the deck, or steaming at 30 knots to make wind on a calm day, the indications to the pilot are identical.  

Contrast that with a HUD equipped aircraft.  The FPM uses the earth as a frame of reference, not the ship.  It shows where the aircraft is going relative to the surface of the sea, its position is based on calculations from inputs of GPS and air data computer, and factors in the wind.  (which itself is calculated…)  It doesn't know or care if the ship you are trying to land on is moving.  Therefore, if the ship is stationary one would expect that the FPM would indicate a touchdown point right in the landing area.  Just as it would a stationary runway on land.  (if the pilot is doing his or her part!) 

If the ship is steaming at 30 knots the FPM will still indicate where the aircraft is going relative to the surface of the sea.  However, since the carrier is moving as well, the FPM will be out in front and to the right of the landing area during approach.  (Because the ship hasn’t gotten there yet!)

In the video you can see that the ship has a decent wake behind it, but as the aircraft closes in the FPM moves from up and right, to right in the landing area at touchdown.  

Keep in mind also that the FPM is pretty much instantaneous, so that pilot corrections to glideslope deviations will show up as well.  For example, if the pilot rolls out high and right at the start, even if the ship is making all its wind the proper correction might put the FPM down and left until re-correcting.

And finally, the Navy discourages “HUD Cripples”.  While (I have heard) it is a wonderful tool, the pilot should reference the traditional meatball, lineup, and AOA on short final.  So while the pilot is supposed to be aiming for the ship, his or her FPM may actually be aiming just a bit in front!  ;)