It seems like the root motion issue I mentioned above could be a bug or a limitation of the animation retargeting. The translation of the root bone is not being scaled to the proportions of the target skeleton.
In the picture below I’ve turned on Show NonRetargeted Animation (so the yellow bones are the source animation) and selected the root bone of the target skeleton. As you can see they’re both in the same place. The new Mannequin skeleton has slightly shorter legs than the old blue guy so the root bone should be a bit behind the source animation.
The skeleton Translation Retargeting options don’t seem to affect the root bone.
Hopefully someone has some thoughts on this please? Maybe Lina or someone else from the animation team will see this when they come into work tomorrow!