Thank you for reporting a bug to Unity.
After reviewing the behavior, we've confirmed it aligns with the current design and intended use of the feature. We understand this may differ from your expectations or workflow.
For more context, the model used in the repro project is imported at a really small scale. To have the real size model, the game object scale is set to 100, but ProBuilder is reasoning on the model scale 1 and thus merges close vertices.
To ensure a good import of your models, please follow the Unity guidelines on models preparation:
https://docs.unity3d.com/6000.6/Documentation/Manual/models-preparing.html
A quick workaround for importing your current model would be to scale the imported model to 100 "before" import. For that, select your FBX in your unity project and change the import settings.
We will close this case as 'As Designed.' If you have feedback on how the feature could better meet your needs, please let us know - we value your input and consider it in future improvements.