I believe your problem is this line allow-additional-properties="false"

allow-additional-properties Boolean. For a JSON schema, specifies whether to implement a runtime override of the additionalProperties value configured in the schema:

• true: allow additional properties in the request or response body, even if the JSON schema's additionalProperties field is configured to not allow additional properties.
• false: do not allow additional properties in the request or response body, even if the JSON schema's additionalProperties field is configured to allow additional properties.

If the attribute isn't specified, the policy validates additional properties according to configuration of the additionalProperties field in the schema.

source: https://learn.microsoft.com/en-us/azure/api-management/validate-content-policy#content-attributes

This property overrides your JSON Schema. Even though your allOf definition does not use additionalProperties: false, apim will inject this constraint to the root schema, which translates to

{
  "type": "object",
  "additionalProperties": false,
  "allOf": [{...}, {...}]
}

This schema doesn't allow any properties to be validated because no properties are defined at the root.

The only valid schemas in this situation would be

{}

OR

true

There are a few ways to tackle this but IMHO, the best option is to use the schema definition, rather than the apim attribute because you're introducing constraints on the schema where they are not defined. If someone else were to review the schema, they would run into the same issue you are having.

This is where it may get tricky for you depending on which version of JSON Schema is supported in APIM and which version you are using.

Draft-04 - 07 requires some massaging to the schema, in most circumstances, to achieve the desired behavior of using allOf with additionalProperties": false

• turn off the content attribute in your apim validation
• add all properties of the first depth of subschemas to the root with an empty schema. This will allow the validator to recognize those properties at the root level to satisfy additionalProperties

{
    "$schema": "http://json-schema.org/draft-07/schema#",
    "type": "object",
    "additionalProperties": false,
    "properties": {
        "messages": {},
        "temperature": {},
        "top_p": {},
        "stop": {},
        "max_tokens": {},
        "presence_penalty": {},
        "frequency_penalty": {},
        "logit_bias": {},
        "user": { },
        "n": { },
        "function_call": { },
        "functions": { }
    },
    "allOf": [
        {
            "type": "object",
            "properties": {
                "temperature": {},
                "top_p": {},
                "stop": {},
                "max_tokens": {},
                "presence_penalty": {},
                "frequency_penalty": {},
                "logit_bias": {},
                "user": {}
            }
        },
        {
            "type": "object",
            "properties": {
                "messages": {},
                "n": {},
                "function_call": {},
                "functions": {}
            }
        }
    ]
}

If you're using JSON Schema draft 2019-09 or later, you can use the newer keyword unevaluatedProperties which performs the behavior described above, automatically.

{
    "$schema": "https://json-schema.org/draft/2019-09/schema",
    "type": "object",
    "unevaluatedProperties": false,
    "allOf": [
        {
            "type": "object",
            "properties": {
                "temperature": {},
                "top_p": {},
                "stop": {},
                "max_tokens": {},
                "presence_penalty": {},
                "frequency_penalty": {},
                "logit_bias": {},
                "user": {}
            }
        },
        {
            "type": "object",
            "properties": {
                "messages": {},
                "n": {},
                "function_call": {},
                "functions": {}
            }
        }
    ]
}

This example fails:

{
    "messages": [
        {
            "role": "user", 
            "content": "Find beachfront hotels in San Diego for less than $300 a month with free breakfast."
        }
    ],
    "stackOverflow": -1
}

Invalid

# fails schema constraint https://json-schema.hyperjump.io/schema#/unevaluatedProperties

#/stackOverflow fails schema constraint https://json-schema.hyperjump.io/schema#/unevaluatedProperties