I am a new user of OGS6, and I have some suggestions about your question.
First, I think, in OGS6, the gml file is better to match your msh file. And if you want to insert a borehole, I suggest you try the Boolean command in Gmsh.
I have some similar files, you can download in this topic.Usage of the constructMeshesFromGeometry tool
More reference about Boolean in Gmsh, you can find in Gmsh manual and Youtube. I hope I can help you.
Best,
-Rui
