I'd try to do everything the way my instructor suggests. You are, after all, paying him or her large sums of money to teach you how to fly: why doubt what they are telling and showing you?
(In the instance you ask about, your instructor is right by the way. The aim is to touch down with the main wheels first at the lowest practical airspeed. This protects the nosewheel, which is easily damaged, and gives a shorter ground roll. These things may not seem important if you are flying from a huge tarmac runway in ideal weather, but that won't always be the case. You need to learn to do it well right from the start.
The aim is not to land as gently as possible! Its to land as safely as possible. They are not always the same thing.)