the stem dosen't have to be at the top of the steerer tube unless you need it there to get the bars to a comfortable height ,
tbh it's better lower down , so the steerer tube sits above the stem a little as the stem will clamp more securely and this will stop the top of the stem deforming , use a single or multiple spacers on top to get the compression , some people don't like the way this looks, some stems also have a recess for the compression cap to sit flush with the top of the stem so you may need spacers that fit the recess , you only need about 1mm to get the compression right so if your running the stem at the top of the steerer try to keep the gap to the top of the steerer tube round about that ,