This is a small but vulnerable spot, and we often see it detailed incorrectly on existing work. Valleys are prone to collecting leaves, particularly if someone sets up an antenna at the base of the valley. The lower roof unavoidably slows down water drainage, and when the valley is clogged, a significant amount of water coming down that valley will tend to spread out and back up under the shingles. Wind can intensify the problem, pushing the water upward. Snow tends to pile up here as well, and ice damming is likely.
Compared with some other regions in the U.S., the D.C. area may not see that much snow. But we've had enough big storms during the last 24 years to make it imperative to detail roofs to manage melt-water and the potential for ice dams.
To protect against water backing up—whether from leaf clogging, ice dams, or even just wind exposure—you need to bring the membrane for the lower roof up about 18 to 24 inches. This is the vertical rise, which means you are running something like 25 to 36 inches up the roof, depending on the slope. Many details call for an 8- to 12-inch vertical, but this just isn't sufficient.
At the roof transition shown in photo, roofers had installed peel-and-stick over the EPDM lap. They had the right idea, but the peel-and-stick they used was rubberized asphalt, which reacts with EPDM. They also didn't overlap the two membranes enough, so it wouldn't have been long before a significant leak developed along the entire length of the overlap.
In the instance shown in photo, the installer left the release paper on to provide isolation. The problem with this detail is that I'm not sure what the life of that release paper is—certainly not as long as aluminum's—so this is a middle-road detail, maybe not best practice. But at least there won't be an immediate failure due to the incompatibility of the two membranes.