Automatic rules have the key "auto-generated" set to true. Try this:
mgmt_cli -f json -r true show nat-rulebase package <UUID> details-level full limit 500 offset 0 | jq '.rulebase[]|if has("rulebase") then .rulebase[] else . end|select(."auto-generated" != true)|.'
Note that this flattens the NAT rulebase so sections no longer appear in the output. It's fine for demonstrating how jq's select statement can filter this, though.
[Expert@DallasSC]# cat testNat.json 
{
  "uid": "fcd91efa-fd33-47ce-9985-aa8afb838fc0",
  "rulebase": [
	{
	  "uid": "01234567-89ab-cdef-1111-111111111111",
	  "auto-generated": true
	},
	{
	  "uid": "01234567-89ab-cdef-1111-222222222222",
	  "auto-generated": false
	},
    {
      "uid": "f364febb-bf96-4979-b8df-5033952173a2",
      "name": "Automatic Generated Rules : Address Range Hide NAT",
      "type": "nat-section",
      "rulebase": []
    },
    {
      "uid": "b63740e8-e228-4ac3-a9ae-43f484415515",
      "name": "Automatic Generated Rules : Network Hide NAT",
      "type": "nat-section",
      "from": 1,
      "to": 2,
      "rulebase": [
        {
          "uid": "01234567-89ab-cdef-2222-111111111111",
          "auto-generated": true
        },
        {
          "uid": "01234567-89ab-cdef-2222-222222222222",
          "auto-generated": false
        },
        {
          "uid": "01234567-89ab-cdef-2222-333333333333",
          "auto-generated": true
        }
      ]
    }
  ]
}
[Expert@DallasSC]# <testNat.json jq '.rulebase[]|if has("rulebase") then .rulebase[] else . end|select(."auto-generated" != true)|.uid'
"01234567-89ab-cdef-1111-222222222222"
"01234567-89ab-cdef-2222-222222222222"