I had the same problem on a Touch Pro 2, I brought it into the Verizon store and told them it wouldn't charge, I did not say anything else. The guy plugged it in conformed it wouldn't charge and ordered me a refurb. He did say that the charging port was not covered under the warranty, but I don't think he confirmed it was the port. If the port is disconnected internally, I agree with you, it is a manufacturers defect. If the pins are loose (which was my case, I can see them having an argument for wear and tear. )
What if another internal part had come loose, it would be clear that its a defect, and since it is the entire port, the disconnection is "inside" the phone.
I think your case is going to depend on whether the guy/girl behind the counter likes you.
If you have no luck at the store, you can always call *611 and complain the screen is sporadically doing crazy things, and they will send you a new one. But be careful, if they figure it out, you will most likely be charged full retail.
Good luck.