When does science and the quest for knowledge end?
Well, actually it ends the moment a supernatural entity can be undetectably altering the results of observations.
Anyway, your answer sounds to me like you just want carte blanche to propose forever that any system whose pathways haven't yet been demonstrated might be IC, and therefore naturalistic evolution isn't yet acceptable to you. That amounts to you setting a bar for the acceptance of naturalistic evolution that can never be overcome.
"And how do you propose to discount the argument that the Designer may be intervening in the petri-dish?"
What is that argument?
The argument that we've had before. Once you propose that a Designer of unknown motivation and powers can undetectably intervene, then how can you ever trust the results of any naturalist experiment. If BF appear in the petri dish, how do you know that your proposed Designer didn't tweak them into existence? Or are you going to set limits on the Motives/Power/Detectability of your hypothetical Designer?
I could submit such proposals till I'm blue in the face, but what would effectively put an end to it is detailed, testable reconstructions demonstrating that such structures can occur in a gradual, step by step Darwinian process, in which case Occam's razor would suffice nicely to finish off a design inference, or at least render it superfluous. One doesn't need to invoke intelligent agency where a naturalistic, undirected mechanism will do.
As far as the methodological approach to the epistemological dilemma of a putative Designer tweaking the Petri dish, I've never heard of anyone not doing an experiment or suggesting it invalid because of lack of direct knowledge or certainty of possible motives/powers of any designer. That type of Humean certainty is not a necessary part of a scientific design inference anyway.
Cordially,