The monkeys at your LBS are idiots.

Why would they cut a steer tube that short before the bike was fit to a purchaser.

The stem should sit clear of the top of the steer tube by between 2.5 and 3 mm - the extra clearance is what gives the top cap the ability to press down on the stem assembly and tension the bearings.

Anything more than 2.5 to 3 mm is too much.

Your LBS is staffed by nitwits - chances are they ruined a fork for nothing more than giving the bike the "racer boy " look.

You could always flip the stem to a riser position, or try an different stem.