Personally, I don't know why having blended branches is such a big deal. (You really can't see the difference from a distance and if its a close up or a tree featuring a lot in an animation you'll probably wan't to get the shape a specific way and do it by hand). Anyway, regardless I thought I see if there was a quick way...
T-Gen and Polygonise.jpg
Here's a quick test I did using emPolygonise demo, T-Gen2 (only a few branches because of polygonise DEMO limitations) and Gator to transfer the UVs.
This gets you blended branches.
However, as I'm using the polygonise demo version I cannot scale the tree large enough to see if I can regain the "tapering" of the branches. (I think scaling the scene up and increasing the T-gen polycount would result in the polygonised version being massive.)
T-Gen and Polygonise2.jpg
Also, I tried using a shrink wrap operator with weightmap driving amplitude on polygonise-generated mesh to try to blend the branches from thin tip to wider base. But for all the time it takes fiddling about you may as well just model in these connections.
Thank you for the presentation. But I try to imagine how this work with dozens of trees... For a few models this is ok, but not practicable for lots of trees. But maybe you are right, no one see the branch and texture intersection it if you are moving through a forest.