From my reading it only effects it’s own trees.
It only replaces Vanilla Trees (and vanilla trees can still spawn and it won’t effect those).
And there are addon mods to replace trees in certain other mods, like Biomes o’ Plenty.
Regardless it only ever effects it’s own trees (trees that use its API specifically*), not even the trees it replaces that can still spawn normally.
So you should keep yours working on any trees that aren’t of one of it’s class type Block subclass.
And heck, you should call it to let it make it’s version of your trees too! That would be awesome!!
Or better yet, subsume it’s functionality! ^.^