You should first align the lasers using the alignment tool, the run the auto-calibration feature. After that do another scan. Is it closer this time?
I found that in practice getting perfectly align scans from the left and right laser is nearly impossible. The Auto-calibrations helps a lot, but even that can't get everything perfect, just very close.
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.