By the way, I done one experiment and find that it's the working way to hide that ugly black bezels on tree LOD:
[spoiler=Picture]
Alpha-Channel stays the same. Background color applied depends only on existing alpha.
Reason of this black bezels is black atlas background. It would be good, if you add a feature to generate tree atlases with correct background, like in TES5LODGen Vanilla Skyrim LOD Billboards (wherefrom I took these colors).
[spoiler=Full screenshots]
Black BG:
Colored BG: