This is not an issue per se; the problem arises because of every tree that's wider than one block uses dynamictrees:trunkshell, but this block has a generic Block state which means that other mods can't target a specific tree shell but has to target all tree shells.

Why is this a problem? It's impossible to define a single tree as a whole to be affected by other mod, i.e. not being able to make redwood harvestable with an iron-tier axe only, since to make its shell unbreakable all trees would become unbreakable too.

Thank you for this suggestion. I'll take it into consideration though the problem you are describing is not likely to be something fixable.

This is an good suggestion. My only problem is with the existing generic shell blocks in the world, how I would handle them.

This may be more work than needed, but a system where every tree "sheds" its generic shell to regrow their custom one could be an option. I'm no modder, so I don't know how viable is this.