After experimenting with this a bit more I found the following ABP template setup much better to work with:
ABP Template
Implementation of UpperBodyBlend
The template now implies a humanoid skeleton so it’s not 100% agnostic anymore, but at least you don’t need to think about nested anim instances for linking. Small price to pay for ease of use.
You still have to link the UpperBodyBlend manually at runtime though. Again, if we could override layers of an ABP template in the child ABP that would make it much better without needing to link it.