The biggest problem is with Attachment Filtering Agent, which does not offer any white-listing. The only possibility to bypass attachment filtering without disabling it is by using separate receive connector and then add it to ExceptionConnectors parameter.
As per Microsoft: "The ExceptionConnectors parameter specifies a list of connectors that should be excluded from attachment filtering. Attachment filters aren't applied to email messages received through these connectors. You must use the connector GUID to specify the ExceptionConnectors parameter value."