Why did my instructor recommend that I fly a Piper Seminole down to the runway rather than trying to flare it like a Cessna?
I'm guessing that is a landing technique that your CFI has developed for handling a Piper Seminole on landing.  Don't worry; everything is fine.

Most likely this is because the PA-44, like it's single engine cousin, the PA-32 and late model Cherokee Arrows rapidly loses energy and sinks quickly once the power is pulled out.  These tend to be the landing characteristics of larger, heavier aircraft.  Cutting the power too early in the approach to roundout could cause this aircraft to slow and drop rapidly leaving a neophyte student with little energy left to flare to a smooth touchdown.  The CFI is trying to make you cognizant of that fact; I'm sure he's endured plenty of firm landings by students with high time in C152s or C172s flying final at 65 KIAS, then chop power over the threshold markings (piano keys) to arrive at a good flare and touchdown; that technique won't work in larger twins and the best way to fly a shallow glide slope is to do so with power, then pull it out just as you begin the flare about 7-10 feet off the runway.  The airplane should then settle into a nice flare 1-2 feet off the runway, quickly exhaust all of its energy and touch down on the mains just as you hear the stall warning tone.

Another factor is the aerodynamic slipstream from the propellers. As wing mounted tractor engines push air over the wings behind the propeller disks, this, in turn is generating additional lift.  During a stabilized approach, this airflow become part of the lift the wing must generate in order to remain on speed at the selected rate of descent.  When the pilot pulls throttles to idle as part of the roundout process, this additional lift is terminated.  Combined with the high drag from the idling low pitch propellers, this causes the airplane to slow down and sink very rapidly; you will feel this in the seat of your pants if you pull the throttles out too early.  If a student pilot remains ignorant of this effect and does not compensate for it, you may be in for a very hard landing or worse.

The Piper aircraft, as you have found out, are designed to put up with a lot of sloppy handling from a new pilot and still shine.  The controls have all the finesse of a Mack truck and they really have to be manhandled to fly them.  IMO it's an attempt by the manufacturer to 'idiot proof' the airplane and make it safe and marketable to a wide range of pilot skill.

All tricycle gear aircraft should be flown to the roundout such that once the flare is established, the airplane should run out of energy and quit flying rapidly.  Strict adherence to a controlled approach speed of 1.3 Vso on final should be used (on small aircraft), but the rate at which the airplane slows and descends when the power is reduced to idle varies between airframes.  Some airplanes do this faster than others; each one has it's own unique handling characteristics and you will have to become familiar with them as you progress through different aircraft.

One note on you flying: for a VFR traffic pattern, aim for the numbers or use an optical glideslope (eg VASI, PAPI, etc), if available, on final until you have become proficient with flying the PA-34.  The 'chevrons' are a blastpad and frangible arrestment for stopping an overrun and are not designed to support an airplane during normal flight operations.  Touchdown too early and end up on the blastpad, it is possible the aircraft could break through and cause damage to the airframe, props or landing gear.  You're also likely to clip other objects like runway threshold lights with that kind of a landing.