I have test the transport rule in my environment and get the same result as yours. This should be an expected behavior. The Exception only works for recipients outside the organization and internal users still meet the requirement so the sender will receive the NDR.
And I'm afraid there is no such automatic way set directly to meet your need.
As a workaround, we could add an exception in the rule you set above: like if the subject include any specify words or phrases. When your internal users want to send mails to both internal and external recipients (meet the attachment size limit), add the specify words in the subject you created above. So the recipients in this mail will receive it successfully.
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