Firstly, it doesn’t provide full and uniform support for the flagstones. Some parts are supported; others are left ‘bridging’ two spots, which makes them more prone to breaking.
Next, those empty spaces between mortar spots are a recipe for disaster. They allow water to pool underneath the paving, which encourages the growth of algae on the surface, but also destabilises the sub-layers, causing some of the finer material to be washed away. This, in turn, undermines those mortar spots, and the flag will start to rock, pivoting on the spots that haven’t settled or shifted.
Furthermore, the spaces underneath the flagstones also provide an ideal hidey-hole for invertebrates and small mammals that will mine or tunnel through the sub-layers, again destabilising the paving and resulting in uneven settlement or broken flagstones.
Finally, with some types of flagstone, the bedding will alter the porosity of the flagstone and visibly affect the surface appearance. This is especially apparent should the Global Sandstone flags be laid in this manner.