Question-and-Answer Resource for the Building Energy Modeling Community
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I found this exchange which seems to provide some related advice specific to envelope+lighting compliance with CBECC: https://unmethours.com/question/998/cbecc-com-envelope-and-lighting-compliance/
I can not claim any practicing expertise with CBECC or recent direct experience with T24, but it does look like auto-sized baseline systems of the same type should be expected. Whether those auto-sized baseline systems applicable to both cases should result in a net penalty I suppose should then depend upon what exactly you're inputting for lighting and envelope, relative to the baseline case.
If the results remain quite unintuitive, perhaps you may find some luck submitting a support ticket here? http://bees.archenergy.com/issue.html
