I don't know anything about that particular bike, but I don't think the kind of thing you are finding is unusual.
I would break it down into two catagories. 1) difference between specs and frame, which is normally a good thing. 2) QC in manufacture.
Where "1" is concerned I just looked at the table, and it isn't my kind of bike so I might not spot anything, but generally the fixed parts like CS length over certain sizes do appear to be accomodated to some degree under the variable items like the HT angle. Quite often the measurements in the geometry trables are for show. But there is some plausibility here.
Where 2 is concerend I would wonder how able you are to measure some of this stuff, just knowing how difficult it can be to get a level to sit on head tubes unless it is the perfect length and there isn't any paint build or head badge to get in the way. It is pretty hard to mis-saw a tube by 2mm in a production setting, so I would tend to put apparent erors down to geometry fuzz. If they are left/right problems, and there are also alignment problems then the frame may have problems. Factory frames aren't built like custom frames though.