Thanks willh, but I was trying to figure this out without using any of the autorig components, and manually setting it up. There is a script you can run from the graph "Update Rest Transforms From Skeleton" that will update those rest transforms.
I did figure out what I was doing wrong after looking at the docs a little more closely.
First, I didn't have the subport names of the SetPointTransforms node matching the joint names of the skeleton as they should. They don't automatically get named correctly when you attach them to the TransformObject.
Second, I had incorrect inputs in the bonedeform node. Base.shp needs to go into geoinput0, and base.skel goes to geoinput1. I had them swapped because that's what the image in the docs appears to show:
I think the way these wires lining up vertically make it hard to tell what is plugged into what in the docs.
