What I keeping finding myself wanting to do is to stack up Scene Animate nodes to layer animation. It seems so logical but all the keys from upstream show up downstream in the newly added Scene Animate. For instance a generic swing on an arm, then add another Scene Animate to add some secondary motion or wave or whatever. How do I achieve this?

The Scene Animate currently stashes all the animation so it's not possible right now. It's on the TODO list to fix this by adding animation layer support. Then channel modifications can work on their own layers in stacked Scene Animate SOPs.

And SideFX added animation layers. Thank you for Houdini 20.5

The animation layers are not "stackable" yet through the APEX Scene Animate SOPs but that last part will come.