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For instance, if you want to theorize about the rise of autonomy in biological life then state your applicable presuppositions first.

What if you don't want to theorize about that? I't submitted that Darwin is to be held accountable for the misperceptions that TToE addresses the origins of life because he didn't explicitly state that it doesn't, and thereby gave everyone license to "fill in the blanks" however they choose.

Again many if not most of the routine investigations are managed by protocols which establish the axioms such as they are for a particular class of investigation.

At the same time, you seem to be saying that there's no reason to be bound by established protocols, or that you have to be constrained by existing axioms. You can declare whatever axioms you want. "Established protocols" are all based on methodological naturalism.

Then you exclude it in the axioms/postulates! In this case, Darwin should have said "This theory does not address the origin of life or what life is."

Because he didn't say that, people do indeed "fill in the blanks."

At the same time, you seem to be saying that there's no reason to be bound by established protocols, or that you have to be constrained by existing axioms.

To the contrary, I'm saying if there is a protocol in place for your investigation - for instance, of an antibody - then it is enough to refer to that protocol.