How does the 
"Modify Chance (If not modified, use default mineral)": 0.0,
work ?

Is it percentage that overrides all minerals or an entry multiplier ?
And what is the scale ?

If modified, it is used "Mineral Items"

        "Mineral Items": [
          {
            "Mineral Item Shorname": "stones",
            "Chance": 60.0,
            "Minimum pM": 90.0,
            "Maximum pM": 150.0
          },
          {
            "Mineral Item Shorname": "metal.ore",
            "Chance": 50.0,
            "Minimum pM": 11.25,
            "Maximum pM": 22.5
          },
          {
            "Mineral Item Shorname": "sulfur.ore",
            "Chance": 40.0,
            "Minimum pM": 11.25,
            "Maximum pM": 11.25
          },
          {
            "Mineral Item Shorname": "hq.metal.ore",
            "Chance": 30.0,
            "Minimum pM": 0.9,
            "Maximum pM": 1.5
          }
        ]

Oh okay, so if you set it to 100 it will only use that entry to populate the crater/analysis.

Thanks :o)