Sort of agree, but this is me, sorry :-). The three alternatives you gave are quite different. I'm trying to avoid sending the guitar back to the seller, since it would take few weeks or more, if possible. But since I promised to deliver the seller some info, I'll show also you "the evidence". See the attached MP3 and few photos. To me the tuner heights seem quite normal as they get shorter towards the lighter strings.
I know I should make a service ticket to get official Line6 feedback on the subject, but if someone from Line6 sees this, I'd be glad to hear their opinion.
JTV69S_EString_Buzz.mp3