Joseph Bolton wrote:
The watertight geometry I've see solutions to deals with the uphill side of a square opening in a roof that would tend to trap water, leaves, and eventually leak, if that makes any sense. Providing a sloped flashing for that flat area of ponding would make the water run off rather than sit until the caulking fails from mildew and age. The leaking roof isn't made a problem because of the skylight, rather, the skylight installation created a ponding location that the builders didn't solve, and that gives the skylight an underserved bad name. Solve the ponding and prevent the eventual leak point. All the other leaking issues are just quality issues and improper application of what is already known how to fix. Preventing ponding for some reason is neglected in this particular case, but even that isn't a totally new problem needing creative solutions. It's just a new geometry issue when you install a skylight that is easy to solve.
So I think the thing you're talking about is called a saddle: it's essentially a big piece of flashing that goes on the upslope side of a rectangular penetration, and it has its own kind of ridge in the middle so water can't pond there. They are fairly standard for masonry chimneys, for example.
So much for water leaks, but what about air, vapor, and thermal leaks?
I did share a video upthread where someone reported that most "leaking" skylights are actually not leaking at all, but rather installed incorrectly, in a way that allowed condensation buildup around the penetration. Curious what you think of that.