I got a call from the local Apple store today. Oh, in regards to Lisa's comment the other day - the woman I spoke to gave me the most comprehensive story, but the voicemail a guy left initially said the same thing, albeit less detailed. And apparently the same thing was put on the invoice when it was shipped back to the store. The repair guys in Texas have their story, and they're sticking to it.
The guy who called today (the same guy I talked to initally) asked what they told me, and said that what was on the slip was totally wrong. The LCD screen spots were completely normal and should be covered, as of course should be the trackpad, and he was going to send it back to Apple to have them fix it. Yay! He apologized that it would be shipped out again, but I don't care about that - I didn't figure repairmen would show up at my house in the middle of the night and fix it while I slept. I'm just glad it'll be fixed.
So all's well that ends well, and also it is way better to deal with actual people you've seen face to face than customer service voices on the phone.