OK - got an update for everyone.
I ended up calling them yesterday because I got slammed at work the day prior and completely forgot. I spoke with Christy in the morning, which works out as she was the one who I'd spoken with initially. She confirmed that they did receive my knife about a week prior, but that the knife was with the production manager Jim, and that it'd take some time for him to check it out. She mentioned turn-around time for warranty work right now was about 4 - 7 weeks.
I told her that was fine, but asked her if she, or anyone had even had a chance to look at the knife yet, and had any insight into the reason behind the patina/rust. She admitted she wasn't the person to answer that, and put me in touch with Jim via social media, who was super responsive, and actually went to grab my knife after I messaged him, and took a look at it right then and there. He reassured me that it was definitely 3V. His plan was to remove the rust/patina first, and then to leave alcohol on those same spots all-day to see if it left any staining or rust again, as that would indicate a problem. His one theory that he mentioned was that it's possible "there were some scratches from a rougher step still in there".
At the end of the day, he got back in touch, and told me that the patina and rust both came off with a fresh buffer pass. He also confirmed that he was not able to make any rust appear with the alcohol that he applied on the blade where the patina and rust had previously been. He let me know that it should be on its way back to me in the near future.
So, i'm not sure if that's a satisfactory ending for those of us who wanted to know exactly why those spots were there, but I'm glad the issue has seemingly been resolved. I'm definitely going to keep an eye on it once I get it back and will report anything worth following up on here. Just some final thoughts - I do wish, or think that there should be a slightly more formalized method of tracking warranties as they move through the process. In this day and age of email and instant correspondence, even an automated message that says something like "We've received your knife, and will have an update for you in 7-10 days, and you can expect the knife back in your possession in 4 - 7 weeks" would be helpful. Both Christy and Jim were very nice over the phone, and via messaging, but some method of updating the customer is probably a good idea. I'll reach out to them with the above suggestions once I have my knife back in my possession.