{
  "X1": {
    "X1o1": {
      "X1o1o1": "abc",
      "X1o1o2": "def"
    },
    "X1o2" : {
      "X1o2o1" : "ghi",
      "X1o2o2": "jkl"
    },
    "X1o3": "mno"
  },
  "X2": "pqr"
}

reduce (tostream|select(length==2)) as $i ({}; .[[$i[0][]|tostring]|join("_")] = $i[1] )

{
  "X1_X1o1_X1o1o1": "abc",
  "X1_X1o1_X1o1o2": "def",
  "X1_X1o2_X1o2o1": "ghi",
  "X1_X1o2_X1o2o2": "jkl",
  "X1_X1o3": "mno",
  "X2": "pqr"
}

reduce to_entries[] as $kv ({}; setpath($kv.key|split("_"); $kv.value))

{
  "X1": {
    "X1o1": {
      "X1o1o1": "abc",
      "X1o1o2": "def"
    },
    "X1o2": {
      "X1o2o1": "ghi",
      "X1o2o2": "jkl"
    },
    "X1o3": "mno"
  },
  "X2": "pqr"
}