I am having the same issue. I have noticed that it only happens in Safari, and in my professional opinion as a software engineer, it is a software issue with Safari. I would say that the problem is due to the way that Safari handles scaling web sites to the high resolution display.
I have not tried this, but one could test this by switching the display resolution to "scaled for more space" in preferences. For the uninitiated, this will turn the "retina display" graphics scaling off, and give you the same 1:1 resolution you would get on a standard Mac display. That may turn off the scaling feature in Safari, and prevent the flickering issue. I would, however, not be surprised if it did not fix the issue.
Hopefully, to allay any/everyone's concerns, when an issue happens in a particular piece of software, but not in every piece of software then it is likely an issue with only that piece of software. I would not allow the Geniuses to replace your hardware in that case. You may end up spinning your wheels with no resolution to the issue.
For this I would just wait for the next release of Safari (as much of a pain in the behind as that is).