更新

以下是我的原始答案的一个版本，该版本已进行了多次修订。与原始文档不同，我只发布了原始文档，以展示如何在JFSebastian的工作答案中获得第一个想法，并且与他一样，该对象返回了对象的非缩进
字符串 表示形式。最新的更新版本返回隔离格式的Python对象JSON。

每个坐标的键dict将按照OP的注释之一按排序顺序显示，但sort_keys=True前提是在json.dumps()驱动过程的初始调用中指定了关键字参数，并且在此过程中它不再将对象的类型更改为字符串。换句话说，现在保留了“包装”对象的实际类型。

我认为不了解我帖子的初衷会导致很多人对此发表不赞成的话，因此，主要是因为这个原因，我多次“修复”并改进了答案。当前版本是我原始答案的结合，还有@Erik
Allik在其答案中使用的一些想法，以及该答案下方评论中显示的其他用户的有用反馈。

以下代码似乎在Python 2.7.16和3.7.4中均保持不变。

from _ctypes import PyObj_FromPtr
import json
import re

class NoIndent(object):
    """ Value wrapper. """
    def __init__(self, value):
        self.value = value


class MyEncoder(json.JSONEncoder):
    FORMAT_SPEC = '@@{}@@'
    regex = re.compile(FORMAT_SPEC.format(r'(\d+)'))

    def __init__(self, **kwargs):
        # Save copy of any keyword argument values needed for use here.
        self.__sort_keys = kwargs.get('sort_keys', None)
        super(MyEncoder, self).__init__(**kwargs)

    def default(self, obj):
        return (self.FORMAT_SPEC.format(id(obj)) if isinstance(obj, NoIndent)
                else super(MyEncoder, self).default(obj))

    def encode(self, obj):
        format_spec = self.FORMAT_SPEC  # Local var to expedite access.
        json_repr = super(MyEncoder, self).encode(obj)  # Default JSON.

        # Replace any marked-up object ids in the JSON repr with the
        # value returned from the json.dumps() of the corresponding
        # wrapped Python object.
        for match in self.regex.finditer(json_repr):
            # see https://stackoverflow.com/a/15012814/355230
            id = int(match.group(1))
            no_indent = PyObj_FromPtr(id)
            json_obj_repr = json.dumps(no_indent.value, sort_keys=self.__sort_keys)

            # Replace the matched id string with json formatted representation
            # of the corresponding Python object.
            json_repr = json_repr.replace(
                            '"{}"'.format(format_spec.format(id)), json_obj_repr)

        return json_repr


if __name__ == '__main__':
    from string import ascii_lowercase as letters

    data_structure = {
        'layer1': {
            'layer2': {
                'layer3_1': NoIndent([{"x":1,"y":7}, {"x":0,"y":4}, {"x":5,"y":3},
                                      {"x":6,"y":9},
                                      {k: v for v, k in enumerate(letters)}]),
                'layer3_2': 'string',
                'layer3_3': NoIndent([{"x":2,"y":8,"z":3}, {"x":1,"y":5,"z":4},
                                      {"x":6,"y":9,"z":8}]),
                'layer3_4': NoIndent(list(range(20))),
            }
        }
    }

    print(json.dumps(data_structure, cls=MyEncoder, sort_keys=True, indent=2))

输出：

{
  "layer1": {
    "layer2": {
      "layer3_1": [{"x": 1, "y": 7}, {"x": 0, "y": 4}, {"x": 5, "y": 3}, {"x": 6, "y": 9}, {"a": 0, "b": 1, "c": 2, "d": 3, "e": 4, "f": 5, "g": 6, "h": 7, "i": 8, "j": 9, "k": 10, "l": 11, "m": 12, "n": 13, "o": 14, "p": 15, "q": 16, "r": 17, "s": 18, "t": 19, "u": 20, "v": 21, "w": 22, "x": 23, "y": 24, "z": 25}],
      "layer3_2": "string",
      "layer3_3": [{"x": 2, "y": 8, "z": 3}, {"x": 1, "y": 5, "z": 4}, {"x": 6, "y": 9, "z": 8}],
      "layer3_4": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19]
    }
  }
}