The whole point of the calibration process is to get the lasers perpendicular to the scanning table, and crossing each other in the center of the table.
The calibration routine puts a cross hair in the center of the image that the camera sees. The vertical line should be pointed to the center of the turntable, the horizontal line should be at the height specified by the software setup value (3.25" default if I remember correctly). Once you have the cross hairs lined up, then you need to line up the lasers (both left and right), so their are perfectly parallel to the vertical line, and they meet in the center, like you see it there (they should appear as a single line). When you think you have it lined up, click the TEST button. You should get an image with a single vertical line in the middle of a black screen.
As far as the calibration piece included with the Atlas scanner is concerned, it was designed to do a couple of things. The tips of the corner points are exactly 3.25" in height, so your horizontal cross hair should line up with the tips, and your vertical cross hair needs to line up with the center tip. So in theory, it works the same as the grid, but the grid makes it a bit more accurate.
FWIW: On the middle picture I have, my horizontal line is only 2.5" above the turntable. That was an early test. It is now 3.25" above it (one and a half rows higher). If you want to get really accurate, you make your grid .25" squares
EDIT:
Here is a tip on camera adjustments.
The camera allows for a certain degree of tilt. To get everything aligned and reduce perspective distortion, the camera should be perfectly vertical, with 0° tilt. So when you adjust the height of the horizontal crosshair, never adjust the tilt, always move the camera up and down on the round shaft it's mounted to.
To calibrate the tilt, go to camera mode, then use something vertical in the image for reference, something that is near the edge of the image. Then tilt the camera until the vertical edge of the object is parallel to the edge of the image.
If the camera is tilted up, you will have a perspective view with a vanishing point toward the top, tiled down, the vanishing point will be at the bottom.
Hope this helps.
To print or, 3D print, that is the question...
SD3 printer w/too many mods, Printrbot Simple Maker Ed., FormLabs Form 1+
AnyCubic Photon, Shining 3D EinScan-S & Atlas 3D scanners...
...and too much time on my hands.
seriously though what version of Slic3r are you using? I used 1.0.0RC3