Every application is different but using stubs allows for pressforming, less destortion at the flange and easy straightening if it occurs. Once the stubs are fully welded you then add the tubes while bolted to a head or fixture. Without them the flange joint is welded last... For this reason some companies blob mig wire around the ports so the flange remains it's full thickness after being plained. The length of a stub can be ajusted or angled and there is no reason one more weld in a multiple piece header has to ruin the look. As with any joint it can be metal finished and polished on stainless or sets to be chromed. Should one not use them the expansion method is still viable for a full primary tube. You may need to adjust them here and there but it's a significant saving in time vs hand shaping each one from scratch. More important is that guys who tack, torch and hammer are introducing carbon at the flange weld. Carbon hardens the weld, increases burn in temp, the possibility of contamination and cracking. You certainly don't have to use stubs and at times I choose not to but they are a viable time and problem saving method.
