OK guys... here's an update.
First, this morning I talked with the service tech, the service writer, and the service manager. I brought along an engine diagram and asked them to explain, point by point, what they did, where these parts are, and how they came to this conclusion. They were, much to my surprise, very cooperative (although why they didn't tell me all this when I picked up the car the first time is a whole other issue... but I digress).
Basically, they put the car up on a rack, and did a full audio inspection top to bottom of the engine (like a doctor with a stethoscope). He said the noise is a rod knock coming from the bottom of the engine. Top of the engine sounds fine. There was nothing unusual from the oil that was drained from the pan... no particulates or shavings that would indicate a serious problem. That said, they did not pull the pan to do any further inspection, explaining that this is a "more invasive" and time consuming (4 hour) job that would not change their recommendation. Mazda typically will not crack an engine because doing so can lead to a variety of escalating issues. In their words, they don't want that kind of liability, so their standard procedure is just to replace the motor (which by their own statements is not that unusual for them... really? Are that many Mazda motors going bad that a flat-out replacement is commonplace? I suppose if it's under warranty, it's the simplest thing to do... but really?).
As to what caused the problem... most likely caused by lack of maintenance or lack of oil. Considering they have done all the maintenance on a consistent and exclusive basis, I've asked them to pull all the service records and give me copies. As far as lack of oil... there are no visible oil leaks, so if there is a lack of oil, it could only be because they didn't fill it enough during regular maintenance (not that they would admit to that). Or another possibility is that the oil pressure isn't sufficient. The tech noted that these engines run on oil pressure... meaning that sufficient oil and good oil pressure is critical to their survival (understandable given their size, loading, and cast-aluminum construction... lubrication and cooling are critical... no margin for error since the specs are so tight).
I also queried a Mazda tech online (
http://Mazda.JustAnswer.com)... very helpful, though it did cost me $18. I walked him through everything I've discovered here, even asked some of his questions of the tech this morning. Essentially, he concurred with my current findings... Since the oil seems clean, there's probably no metal shavings or damage to the core, and that at this point it most likely is just a bad rod bearing. Of course, someone still has to pull the pan to find out for sure. So... best case, it's like Davicho says above... pull the pan, find out what's gone bad, and fix it (I think I would replace the oil pump too just to be sure). Worst case, they find metal bits inside, and it's pretty much DOA, but given that the sound has only just recently appeared, and isn't constant, the damage is likely not anywhere that severe (yet).
So, for now we park it until I've had a chance to go through all the service records. Assuming that there is a solid record of performing all recommended maintenance at appropriate intervals, I can state my case to Mazda Corp. and see if I can't get them to give me a new engine. If for some reason my maintenance record has any questionable holes (like not getting an oil change within the factory recommended service interval), then I'm on my own, and need to find someone trustworthy to crack it open, have a look, and assuming things are not as dire as Mazda says, do the repair.
The real question now is... do I still care enough after all of this to want to deal with it... or do I just dump it and run away?