A naturally-created biology is constrained by the natural laws in our universe so cannot look like anything. We can test any natural explaination against observed natural laws.
A supernatural-created biology on the otherhand is not constrained by natural laws, and therefore cannot be tested. It could literally look like anything and not be a contradiction.
What requirement do you think the ToE places on biology?
The two simplest are that organisms can self-replicate and that replication is not perfect. These needn't be true under supernatural created biology but are critical for the ToE.
The ToE only remains standing because a naturalistic explanation is required 'a priori' in order to be 'scientific'. That was the point.
But there is a methological reason why that is so. It is because supernatuaral explainations cannot be tested and so their validity can neither be strengthed or weakened. Allowing them to be entertained as part of science would therefore waste time with no benefit.
If you are looking at a supernaturally-created universe and life, to limit your explanations to 'naturalistic-only' guarantees that you will get the wrong answer.
And entertaining supernatural explaiantions as well will only mean you never reach an answer.
In this case you would only get the right answer if you assumed the supernatural explaination.
Oh, I see. Apparently you require that a supernaturally-created biology must consistently operate through supernatural effects. That would be your error.
Self-replication and imperfect replication are perfectly consistent with a supernaturally-created biology. No requirement for no or perfect reproduction there.
Evolution's purported 'events' occurring thousands, millions or billions of years ago likewise cannot be tested. The evidence supposedly 'supporting' evolution is also consistent with a created biology that is in decline. Nothing there.
Entertaining supernatural explanations as you understand them might have that effect, but a supernaturally-created biology is not required to operate as you imply, therefore there is no reason to think that you can never reach any answer.
Your arguments are only valid by *assuming* they are the only valid restrictions, no way to test that. But then you have moved into the metaphysical realm yourself, so what were you saying?