The short climb uses root motion to move the character so it is based on the animations. For this scenario you'll need to use animations that are at the proper height of the object that the character is climbing.
It was not the root motion exactly. It looks like the animator did not know what to do with the height of the object I was trying to climb. Perhaps it did not fit any of the animations? The value it was being fed was 1.189724. This seems to have confused the animation controller.
I fixed it by modifying the height being fed to the controller by a percentage. This way the controller still grabbed the correct animation, but allowed it to be used with smaller (or taller) characters.
The character was 80% of the height expected. Because the animation scales with the character's bones, it was always off.
To get the animation to work right I changed line 72 inside CanStartAbility() to
m_Height = m_Transform.InverseTransformPoint(hit.point).y * this.CharacterHeightMod;
For this character CharacterHeightMod = 1.25f. I can use different values for different characters at different heights to allow them to match up to the animations.
What is great is this also fixes the issue I was having with the animation on the smaller steps. Before this she would place her hands inside the block, then her feet would be inside the block, once the animation was finished (and it renabled the collider), her feet would pop on top of the step. Now it works correctly.
Perhaps in a future update, you can make your controller friendlier to characters who have different heights than Nolan? Feel free to expand on this change.