I found a solution, dropping it here in case anybody needs it.
The issue was that when I first imported the original skeleton (of the skeletal mesh asset, not the animation) my root was not centered properly. Now, I had fixed this in the FBX, but it wasn’t applying in UE. This is because the “Update skeleton reference pose” option for import settings is disabled by default. So every time I updated the skeleton, everything got updated, except the reference pose. I guess this messed with how the root motion was calculated. Checking the box for updating the reference pose and reimporting the skeletal mesh immediately fixed the issue.