You can't assume things you don't know.
X-Plane itself is responsible for the rendering order. We can only do so much within those bounds. Complain to Laminar if you wish, but they'll basically tell you "Ya, we know, tough luck for now though."
You have no idea how SkyMaxx Pro does scene rendering, so for you to assume something should be so easily done with regards to separating lens flare from clouds is not reality. And, in years and years of production, I think you're the first person I've heard even complain about this (probably because most people just fly instead of cinema).
Our main concern is simmers first. You do nice work, but we have to be practical and economical in approach. Attempting to change something just for you even if you could would not be a smart or viable business decision!