A gantry set up will be significantly less rigid than the conventional column setup, and this will affect the tolerances of the product. Also with a gantry the motors have to move the very heavy spindle around, this means more expensive, powerful motors must be used and also more wear on the linear axis parts such as ballscrews and slides. In most cases for these benchtop cnc machines the product being cut out it much lighter that the spindle setup so it is logical that the stock is being moved not the spindle. Also the counter argument being that in conventional setups the spindle still has to travel up against gravity, however this can be overcome with a counterweight where as on counter weight can be used to offset spindle weight in a gantry setup.
I hope this is helpful, but im an no expert, im still learning.