Mechanical Advantage

An over-table rail system yields a better mechanical advantage.

Shown on the left is the under-table leadscrew system that is used on many homemade CNC tables. On the right is the above-table leadscrew system that is used on the tables in these plans.
Both of the machines have the same Z clearance above the cutting table.
The primary X axis force and load components are in red; these are the X lead-nut, all lower bearings and the bottom Y rail. The fulcrum is the bearing assembly.

The force that is applied by the leadnut to the load has to be transferred through the ends of the gantry. The taller the gantry, the longer the lever-arm that exists between the force and load. This is shown in the lower images.
The gantry will have a tendency to rock on the rails since the Z is so far above the bearings (the fulcrum).

The extra lengths of wood combined with any looseness or flex in the components will produce chatter and greatly diminish the quality of the work and the allowed cutting forces.
In an over-table system the distance between the load and force is shortened, which helps to lessen these problems. It also allows less expensive homemade components to produce better results.

The over-table rail structure offers other advantages as well. It uses less material since a lead-nut support is not needed to tie the ends of the gantry together from underneath the cutting table. This space can be used for other components such as a vacuum hold down system. Also, the gantry end plates can remain above the work, so they will not limit the size of the stock.