I think my disagreement with Kojonen’s argument can best be encapsulated by these two sentences from Glass (who Kojonen cites for an explanation of his argument):
How might conjoining design with evolution provide explanatory gain for the explanandum in question (biological order and complexity)? Basically, by making the explanandum more likely to come about than it would be otherwise.
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This seems to be tying Kojonen to (at least implicitly) accepting older, generally discredited, Creationist arguments that ‘evolution is too improbable to have happened’ (without designer/divine intervention).
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Assuming an omnipotent designer who wills it to happen will raise the probability of any improbable event to 100%. Yes, this means that you can argue that the designer gets (at least partial) credit for evolution, but it also means that the designer is also on the hook for every improbable and unfortunate event – every bizarre automotive accident, every unfortunate coincidence, etc, etc. This line of reasoning also seems to conflate probability (given an unfalsifiable assumption) with plausibility.
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If you cast the net far enough – and evolutionary history of hundreds of millions of years, over the entire planet, would cast it very far – you will inevitably catch some very improbable events. So it does not seem to reduce Evolution’s plausibility if it involved some very low probability events. If somebody told me that all the events that led to the current biological diversity had a probability of greater than 50% (or even 10% or 1%, etc), I would have the very strong suspicion that they were falsifying the record. This is further reason not to conflate probability with plausibility.