I’m assuming that you did your commercial work in a TAA C172 with little or no time in Piper airplanes prior to beginning multi engine training in a PA-44, correct? That might explain why flying the Seminole seems so different.
Most Piper singles and twins like a little bit of manhandling on final and during the roundout; not a whole lot finesse here. The PA-44, which is essentially a twin engined Cherokee Arrow, is going to probably fly a lot like its single engine cousin does. They are really power dependent and, once you pull the throttles to idle, they’re going to drop like a brick. John K points out some of the reason it the drag from the two essentially windmilling props, but again this is just a Piper retract thing.
As to aimpoint, you need to revisit your goals in the roundout: arrest your descent and place the airplane in the correct attitude for landing. Arrive at the roundout at the correct approach speed specified in the POH or no lower that 1.3*Vso to minimize float. Your instructor’s landing techniques are fine, though I would not say “throw out everything you learned about landings from a Cessna”; the techniques still apply but every airplane out there has its own specific performance quirks.
A more critical metric here is touchdown point and that’s dependent on how long the airplane will float in the flare. Try this: on your next pass in the PA-44, when on final, trimmed up and power set for Vref and on glidepath, aim for the first stripe on the runway to enter the flare over. Keep tabs on how many runway stripes the airplane floats over during the flare and note which stripe the airplane finally touches down on. Since each stripe is 120ft long with an 80ft gap between them, you can quickly determine the distance of the float and pick your aimpoint in front of it accordingly.
Remember, don’t reference your aimpoint based upon features in the cockpit, reference it based upon whether its moving in your field of view on final. If you're heading for the aimpoint it should be fixed in your field of view and only increasing in size.
Typically you will smoothly reduce power i.e. pull throttles back to idle over ~1-2 seconds just as you enter the round-out. This is a pretty good technique in Pipers and yields a smoother touchdown. Just be ready to pull back on the yoke as you simultaneously reduce power in the flare as the nose will quickly drop otherwise. Unless you’re flying a seaplane, don’t keep power in during the flare. It only increases the float and eats up more runway needlessly.