Regarding your challenges of what a doctor or chemist would see could they inspect the "post-miracle" effects of the healed blindness or newly created wine respectively ...
I think we all here would accept as undisputed that: miracles (whatever they are) have an effect on the physical world. Right? And that means that their results are (or would be if we were there) available for scientific inspection. And that even for those not immediately there, the results are still there for inspection later (such as friends of the formerly blind man visiting him at a later moment.)
Given your presumed agreement with the above, in what way would you expect the results to appear "deviated" from "normal" things? By this I mean, wouldn't we expect any ideal healing to be a return to normal operation of eyesight --i.e. his eyes would be normal to any inspecting optometrist? Imagine somebody today being healed of heart disease. Suppose that God decided to "show off" in a way that couldn't be mistaken and instead of making a person's heart heal and function as it would for a healthy person, he instead decided to make all the person's blood supernaturally bypass the diseased (and still non-functioning) heart and just miraculously keep coursing through the "healed" person's body. Would we be impressed? I suppose all of us having arguments about science and miracles would be impressed, but the "healed" person might be understandably a little distressed about the situation. My blood is circulating sure enough, but I can't see any compelling reason why it should keep doing so! When we pray for healing, don't we always mean that we would like all our organs to be functioning within normal parameters? In short, we don't expect to find some lingering signature in the results that shout "this is miraculous"! That signature is instead written in the fact that it happened at all, when it did, and with the efficacy that it had, and perhaps as a result of prayer.
Your wine example might supply a different slant here, but let's inspect that too. Here we would be less disturbed to discover that the wine was different. In fact we're told it was different than the formerly served stuff in that it was better! But was it categorically different? The steward still recognized it as wine --good wine at that. How would he know? He must have tasted good wine before. Had this wine had properties unlike any other wine ever had, we should probably expect the steward to be confused or put off rather than impressed. I.e. whatever properties really good wine had back then, the story conveys to us that this particular wine had those properties and was thus unsurprisingly enjoyed by the guests. Why should we expect any visiting chemist to find something different about this wine than any other high quality wines they had? The miracle was manifest in the method of provision, not in (I propose) in the properties of the substance provided (save in its exceptionally fine, but still recognizable quality).
This brings us to your (still unaddressed) challenge of "apparent history" in the wine. You argue that the chemist seeing normal water in a pre-inspection and normal, if very good, wine in a post-inspection would then have beheld something with an apparently "deceptive" history (at least on the reading of the deceptive-God arguments that you object to here). Does that about capture it?
I wonder if we can address it with a parallel situation: a rock innocently perched up at some high point on a hill. It's location there is noted and documented by observers (It's a very interesting rock, apparently). But then people wake up one morning to find the rock resting innocently at the bottom of the slope. Argument ensues over whether the rock was miraculously relocated there, or whether "natural" explanations suffice to explain its locomotion -- perhaps some part of its support structure broke, or something shook it loose
and it rolled down where it is now. OR -- maybe during the night I snuck up there as a prank and carried the rock down and set it in its new perch. In the latter case would we say there is a "false history" now associated with the rock? Where a rock would normally have just rolled and fallen, it was instead "supernaturally" carried there. Would the townspeople be misled if they looked for evidence (perhaps fresh impact marks) on the rock or its alleged path of descent? Should they expect to find such evidence? Not if I carried out my mischievous deed carefully. But otherwise, yes; they should very much expect to see that evidence there.
What people here (whom advance the 'deceptive God' argument you find objectionable) are seeing would be like this: I did indeed sneak the rock to where it is now, BUT I went back up to where it was and carefully crafted marks of violent descent all the way from where it was to where it is so that any careful inspection would conclude (falsely) that the rock had simply fallen to its present location. You can dispute that such marks are being correctly interpreted to find such a long history, but the vast majority of scientists agree from many different consistent and convergent lines of evidence that those marks are indeed there.
Now ... you go on to object (in my particular 'rock' story): but what if I come forward and admit my deed to the townspeople? If I tell them what I've done (like the Bible telling us), then surely that puts a new perspective on the matter, right? Presumably, however, I'm also willing to explain to them why I felt a need to go to such lengths to fabricate the situation and fool them too. [I must have had a real change of heart over something to make me 'fess' up.] But what if I did not make myself available for any such confessions? What should the observers conclude? Which explanation is less conjured?
You propose that the Genesis passages could at least represent just such a statement to us that this is how it was done. Is it possible that you or others or any of us misappropriate such passages? Quite so. Is it also possible that we misinterpret scientific evidence -- converging evidence from many different branches of science? Also possible. Putting it all together which of all this seems most likely? You are correct that we are not always good judges of "likelihood", so we can always play that card to shunt past all logic or evidence if we really feel driven to do that. But hopefully you see why so many here see a much less conjured path that commends itself as a reasonable conclusion.
We [the believers among us] don't get overly concerned about how God's works might be "trumping" God's word. They are both from God --and any contest we try to inject between them is a contest of our making, not of God's. If one appears to "trump" the other more often, this is only a reflection of our access and ability to process different kinds of information from two very different kinds of sources. If you are given instructions by somebody about how to walk to a nearby grocery store (... then turn south on 2nd st. ... ) and you proceed to walk that path; you don't worry about how your eyes seem to be trumping the received instructions more often than vice versa. "I was told to walk south along this road, but my eyes are now sending me a minor corrective to divert this way just a little so as to go around this obstacle." Should the errand-runner conclude that the original direction-giver didn't know what they were talking about? --as if the directions had to be robotic instructions that alone would suffice without any more information input whatsoever? Of course not! We agree that would be silly, and that it is expected and normal that we would use our eyes (science) for daily small and large information input wherever we can, and that this usefully and necessarily supplements the over all directions given (e.g. Scriptures) that we also have. The exhortation that "we walk by faith and not by sight" is not an instruction to close our eyes as we walk. It is an exhortation to keep being faithful even when our eyes fail us.