I found a workaround for this issue. What I did was overwrite the settings.yml file with the one from the second set of pixel hexes and it imported fine first try using the folders from the x96 branch. Not ideal but worth trying if you have both sets, or an older version of the first one.
@zeshio would it be possible to look further into the issue? I don't have the competence to try this workaroundand keep not being able to use the tileset