I'm just a beginner but I can say that there are similar reasons for different setups with spinning gear as well. Sometimes it is all about what you want the fly to look like to the fish. A bead head or heavily weighted fly is created for the sole purpose of sinking at a certain rate. Other times it is used to keep the fly down at a certain level in a given (estimated) current. For bass fishing and for many other species, the weight is applied forward (higher on the line) to give the lure or bait a different presentation. When bass fishing or coastal fishing, one doesn't always want the lure or bait on the bottom so the weight is moved according to the desired depth. I like to use bead heads when I want a fly to have a faster sink rate in faster currents. Like most people, I don't want my flies to reach the bottom but I want it to reach an acceptable level for feeding fish. Water temperature, clarity and current can all determine my desired results.
Sometimes I want the fly to sit in a certain position in the water no matter how long the fly is in the water. This is a good time to use split shot. Lets say I want my fly five or so inches from the bottom of a really slow moving river but I don't want the fly to sink to the bottom. I will place a properly weighted split shot eight or nine inches (give or take) above a non-weighted or light weighted wet fly. Now my fly is above the river or lake bottom and moving with the currents because the split shot is sitting on the bottom and not my fly. Of course this is in ideal situations. Unless the current is fairly fast the fly will eventually sink. This is the whole premiss behind the carolina rig. The fisherman doesn't want the worm on the bottom of the lake but suspended at about the same level throughout the retrieve.
What most people are saying is that you can take a subsurface wet fly and alter it's appearance according to the situation at hand. I say carry one bead head and one non-beadhead. The reasoning is fairly simple. You can get each fly to catch fish at any given point in the water but the both sink differently. I non-weighted with a split shot added to the line does not sink or suspend the same way a weighted one does and vise-versa. Sometimes it is better to have the fly sink on its own and sometimes its better for the fly to be carry down by the line. Situation will usually dictate which is best.
I think it is a matter of preference and available options. By cousin is a guide in Texas and he will say "its not what you have in the box that counts. Its how you use it" At the same rate, I believe that not all fishing is equal. This past saturday a guy out fished me because he was a lazy fly fisher. We both were using white woolies but he used a split shot maybe five inches above the his fly. I used both weighted and unweighted woolies. He caught double of what I did by simply tossing the line 10-15 feet and letting it sit. The split shot was keeping the line on the bottom of the river but his wooly was just sitting suspended off the bottom in the current. Nothing he did was pretty or artistic but if your life depended on what you caught - he won. Not really what most of us consider fly fishing but it caught plenty of fish.
