You are absolutely correct in that your scan results are affected by all the aforementioned variables, primarily laser calibration and lighting.
Unfortunately, the reality is that achieving the kind of repeatable accuracy you're asking for, is going to be hard to do, because of the many variables inherent in the design.
It's a DIY scanner, so there can be lots of small variances from build to build that will account for the differences in resulting scans.
This is a tabletop scanner, which means the lighting source will be different from user to user. This alone will account for 75% of all the discrepancies you see in reflectivity, color accuracy, and completeness of surface (missing parts)
The laser calibration, or lack of it, will account for the dimensional accuracy.
Camera focus will account for the surface resolution and accuracy.
Last but not least, laser scanners such as the Atlas have problems seeing certain areas, blind spots, and will require multiple scans from different angles to get most of the surfaces scanned. Changing the scan angle will also affect the lighting (as seen by the camera), which means that even if your resulting point clouds are accurate, the color map (texture) will be different from model to model.
You could control the lighting by buying a photo box or tent with built in lighting, which would definitely help, but it's still no perfect solution.
As for a standardized model, the bunny would be a good idea, IF we could all have access to the same object. The scanned version on the provided links is pretty devoid of fine details or color information so it wouldn't help much here. Additionally, printing a 3D model for the purpose of scanning it, will yield different results due to the differences in printer capabilities.
Maybe if we could figure out some common household object that everyone has. Or better yet, some common, inexpensive that can be purchased in a store, like an action figure or something like it.
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.