Leaves and logs are recognized if they inherit from LogBlock and LeavesBlock, but some mods don't do that.

This has changed as of Minecraft 1.16. I will have to develop a more complex heuristic to determine logs and leaves.

Some modded trees also droop down, causing branches to be missed.

From ThePsylent on CurseForge:

So I think I figured out why certain trees leave behind their branches! The Biomes You'll Go redwood tree is a great example so I made a short video showing what I'm talking about. Basically, Fabric Tree Chopper scans for connected logs per layer from top to bottom which separates logs that branch downward diagonally. Those logs are no longer seen as part of the tree when FTC starts chopping the next layer down.
https://www.youtube.com/watch?v=M4sYJCcdBlQ