I‘ll offer up some thoughts, but am not quite following; you say you picked up a used one, didn’t bond with it, so you returned it and got a brand new one. Or did you put “new” in quotes because it wasn’t brand new, just new to you and as opposed to the other used one? If the second one was also used, then makes more sense why there could be issues. If the second one was in fact brand new, and if the action was too low to begin with(not sure I’ve heard that ever being a case, usually too high), then I don’t think shimming the saddle was the solution. Might have been a return candidate as well.
Though you updated your post to say you took it to a repair shop, so not the store you bought it from.
leads me to believe it was also used. (People always say I should have been a detective.(insert inside joke here: then I could be working in shifts
))
I digress, anyhow, bellying is from too much moisture, it causes the wood to swell. And if the bellying starts in front of the bridge, dropping the bridge pins downhill so to speak, I could see that maybe pulling the action lower. Dryness will cause the wood to shrink and crack, and it would raise the action if the neck is diving into soundhole. Be easier to spot. If it was in fact that dry, it could also have cracks, and it would seem the frets would have also been sprouting, next question is were they? I suspect not since you said it was bellied. In general if they are dried out, yes, then definitely need to loosen tension, and humidify it. But more likely it was bellying due to too much humidity and you added more! Thinking out loud I would posit that a saturated guitar would not ring out and vibrate as one in it’s sweet spot of moisture content, and could explain why you feel it’s a dud.
Although I’d have started by checking the neck’s relief first, then saddle then nut. Was it just the action initially, or was it also the sound/ tone you didn’t like? I’m wondering, since now in the time you’ve had it, you took it to be checked out and was deemed to be fine, but you still aren’t happy and think it’s a dud. Is it just the action still? I’m unfamiliar with a plate mate, what does that do? Slot the pin holes? Egads, I’ve never had to do that, and thats typically only if your saddle is so low you need to but I feel like it all may have been unnecessary work done to it, as it shoulda played reasonably well right from the jump and if the action was trouble, I might have returned it. Typically a saddle should be lowered not shimmed. If it needs to be taller, recommend to carve a new one. The shim has a better chance of lessening vibration transfer which contributes to lousy tone. Possibly could be a relief issue, but again your tech looked at it. I mean I guess it could be your playing style, but you have other guitars you feel are fine. Have you had others play your F40 and you listen from the other side? How’s it sound when you’re not playing it?