Unsupported geometry type: Polygon / CDT update; point location not in face but on vertex.

[gmorass]

Hello, I've been trying to run 3dfier on a small area of the port of Trieste but get return warning messages:

Geometry type is not supported: Polygon
CDT update; point location not in face but on vertex. Point (index 4); 403199.156 5058315.000 3.451
CDT update; point location not in face but on vertex. Point (index 2); 403199.188 5058315.000 3.141
[... for hundreds of thousands of points]
===== CDT/ =====
CDT created in 75 seconds || 00:01:15
...3dfying done.
CityJSON output: output\tent2.json
Features written in 2 seconds || 00:00:02
Successfully terminated in 80 seconds || 00:01:20

The resulting file is an empty json with one weirdly shaped object. Tried obj as an output with the same configuration and I do see the portion of the territory with holes corresponding to the building sites.
The input shapefiles for the building and terrain polygons have been created with the difference tool as suggested on the documentation and checked on QGIS with the geometry checker for geometry validity and waterproofness. The ID fields are unique and have tested the config file with the YAML validator. I had rarified the input point cloud to make use it more lightly

I have attached the configuration file and the input polygons in case they could help understand. I am thankful for any lead on how to proceed with this.
Giacomo
Shapefiles
test1.zip
YAML configuration file
porto3.txt