As I'm primarily a photographer, I'm not sure of the exact masking and layer methods you have available for that shot, but it's often best/easiest to use overlay/mulitply/grain merge/hard light/darken only etc, type layer modes in these situations. With a typically-blown sky these modes becomes extremely effective with only really a horizon grad to the mask needed. Edge and contrast detection type masking tools that attempt to follow complex and small outlines such as foliage, will strugger to convince the human eye effectively in my experience (and I usually have much more leeway due to typically working at much higher resultions than the vid guys too).
While a simple grad in a normal layer mode would have a wierd fade as it transitioned across the tree, depending on the scene, one of the modes above (and plenty more too) will allow the original outline and detail to show through, without any complex algorythms and frame-by-frame tracking needed. You'll have to play around of course as every scene/layer affects things differently, but in a typical scene where the sky is pastey/blown as a consequence of achieving better forground and subject exposure, it's very easy just to use something like the darken only mode on the new sky layer and tweak the curves for quick and effective results.
If I were to be compositing this scene myself, I'd make sure the sky and city were on seperate layers to facilitate this. Not sure if yours were or not, but just thought I'd throw that in there in case it's useful to you.
YMMV so it's worth experimenting, as with everything. And of course, if none of this is relevent then feel free to uttery ignore me.
The Mocha work was pretty cool too btw. I've not really had much of a chance to play with it tbh, as I keep getting sucked into my Source Filmmaker animation and modelling projects, but I could see the potential in it. There's only so many hours in a day to learn to use yet another piece of software! (and it's looking like it might be Blender next.... ugh). I was toying with the idea of doing a web series too, just for fun of course. It will probably on a comparably non-existant budget to yours too, so I'm certainly looking forward to seeing what other uses you find for it throughout the series.