Regarding the question of the biological reason for this proposed regulation, my guess is that the reason is not biological, but rather sociological. Recreational fishing is intended by most to be sport fishing. Inherent in the concept of sport fishing are ethics that include the rules of fair chase. Fair chase in fishing means the fish willingly takes a bait or lure into its mouth. Fair chase does not include the practice of ripping hooks through the water column with weight strategically placed to increase the likelihood of foul hooking a fish.
There is some biological benefit to reducing snagging. A lot of fish that fall victim to snagging are poorly hooked and not landed, leaving many wounded fish in the rivers. Most probably survive to spawn, but some certainly become infected, and that's a poor testament to sporting ethics.
Regarding the definition of a leader, WDFW needs to apply more thought. A 48" leader to a swivel and weight is a lesser flossing rig than a leader that is longer. But if the definition of the leader says nothing about the weight, then I see a problem. For example, we are not allowed to place the weight below the hook, which would facilitate snagging. But what if a prospective snagger attaches his hook to a 12" leader to swivel and then attaches the weight to a 24" dropper, that is then between 12 and 36" from the hook, but also is a superb snagging rig? I think it might be harder to define what is or isn't a snagging or flossing rig in writing than to recognize one in the field.
Regarding the effects of the regulation on fly fishing, I wouldn't worry about it. Fly fishermen fishing with a sinking or sink tip fly line usually use a leader between 3 and 4' anyway, so that's no big deal. Sure, there are exceptions to using leaders longer than 4' on sinking lines, but see the part about this being no big deal. If a fly fisherman wants to participate in this fishery, then they can suffer the "hardship" of a 48" leader. When fly fishing with a floating line, leaders of 9' or longer are the norm. However, a floating line with a 9 or 10' leader is not likely to be anyone's snagging or flossing setup of choice, so again, I don't see any big deal.
Regarding the notion of simply enforcing the regulations already on the books, just because the LEO says an angler was flossing or snagging doesn't mean the judge will grant deference to the agent. Writing citations and getting convictions aren't the same thing. I think the object is to have clear and simple regulations such that citations written = 100% convictions so that agents aren't wasting what little time they have when patrolling the summer/fall snagfests on local rivers.