I thought that multiple fluid inputs/outputs were just for the sake of symmetry, but they actually affect throughput when the buildings are legendary, beaconed and handle enormous amounts of fluid (most noticeable with steam condensation on Vulcanus).
A steam condensation plant connected via pipe to an acid neutralisation plant (one output connected) will chug regularly due to ingredient shortage even though there's more steam than it can consume. Connect the second output, and it will get twice as much steam, still chugging though. Connect the second input and it will work even faster. And direct connection without pipes gives the best results.