How would you recommend installing this flooring over a floor drain?

To install over a floor drain, or around any other obstruction, you'd simply use a sharp utility knife to cut out the access that you would need to install each tile. Because some tiles need to be installed in a specific orientation, it is best to install the tile first and then mark the cut you need while it is interlocked with the rest of the floor before making any cut. Then simply use a utility knife or a rotary cutting tool and straight edge to cut the tile.