Flanges on valves, pumps, turbines, heat exchangers, etc follow this convention. That's why pipefitter's "two-hole" flanges when fitting-up. Typically, the pipe being worked on is horizontal, in stands or a tri-stand, and levelled, if welding. Flanges being installed by whatever joining method are oriented such that studs or bolts inserted in the top two holes (the flange face being vertical) are true horizontal when a level is laid across them. Since flange bolt holes are symetrical, the holes will line up when it's time to join things together.