Simple monoband quads can set any element to zero and count from that point. Once the loops have been constructed in a free space environment, adjustment for height above ground is a simple matter of changing all Z-coordinates by the same amount. Of course, the amount will be the height above ground if the height represents the loop center. Other adjustments may be needed if the height represents the bottom of the lowest wire. Despite a few remnant protestations from a few quad designers, antenna modeling programs have proven very effective and accurate for designing and analyzing quads.
All programs have some limitations, so let's note the most important ones.
The standard method for reducing this effect to negligible amounts is length tapering. Length tapering can be manually or automatically implemented, and the automatic systems can be visible or invisible to the user who does not look at the post-run wire tables for the antenna. It is a process of reducing the length of segments gradually as corners are approached so that two conditions are met. First, the segments closest to the corner are very short without exceeding the minimum segment length, either absolutely or relative to wire diameter. Second, the changes in length from one segment to the next are within the boundaries set for accurate output from the core.