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Duplicate schema coming from nowhere

See original GitHub issue

Before filling a bug

have you checked the faq for known issues.
have you checked existing issues

Describe the bug

I am getting the following duplicate schema issues:

  error   | PreCheck/DuplicateSchema | Duplicate Schema named 'KeyVaultProperties' (4 differences):
    - properties: {"keyName":{"x-ms-client-name":"KeyName","$ref":"#/components/schemas/schemas:36","description":"Name of the Key from KeyVault"},"keyVaultUri":{"x-ms-client-name":"KeyVaultUri","$ref":"#/components/schemas/schemas:37","description":"Uri of KeyVault"},"keyVersion":{"x-ms-client-name":"KeyVersion","$ref":"#/components/schemas/schemas:38","description":"Key Version"},"identity":{"$ref":"#/components/schemas/schemas:63"}} => <none>
    - type: "object" => "array"
    - items: <none> => {"$ref":"#/components/schemas/schemas:35"}
    - x-ms-client-name: <none> => "KeyVaultProperties"; This error can be *temporarily* avoided by using the 'modelerfour.lenient-model-deduplication' setting.  NOTE: This setting will be removed in a future version of @autorest/modelerfour; schemas should be updated to fix this issue sooner than that.

Looks like it is comparing a model (here) and a property (here). I am not sure if the x-ms-client-flatten is involved or not, but it looks like to be involved.

To reproduce, you need to

change the version of autorest.csharp here from 3.0.0-beta.20220426.2 to 3.0.0-beta.20220426.4
go to this directory and run dotnet build /t:GenerateCode

Expected behavior

We do not have a duplicate schema previously, therefore we do not want a duplicate schema issue if we did not change the swagger.