Hey Kevin,
you don’t mention whether you checked the machine for rectangularity and coplanarity, but I would say, to consider a gantry-type CNC machine (with its two Y axes) as ready to use, these are checks that are necessary, because if the machine is twisted or a parallelogram, flattening the worksurface will not help. If the machine is twisted or a parallelogram, it can only produce twisted or non-square workpieces.