The purpose of tramming the head is to make the spindle axis perpendicular to the direction of travel in the x and y directions. This permits an end mill or facing tool to cut evenly at the front and back. An out of tram spindle will also cut scallops on a face
Tramming is not necessarily accomplished by tramming to the milling vise or even to the table. If the table surface is not parallel to the x and y ways, you will have a false indication. To avoid this, I would fix a plate to the table and lightly skim the surface with a small diameter end mill. The reason for the small diameter end mill is to minimize the scalloping effect. This creates a surface which is parallel to the x and y ways. Then tram your spindle to this surface.