'Starting over' each era is somewhat intentional - I may have overshot it as a consequence of wanting to prevent snowballing. I could make it so that the UA does not trigger WLTED day from GW/conquer/founding. Instead, you'd just get the Mandate of Heaven yields every time you settle/conquer/GW, and then the WLTED day bonus would only come into play through natural means. De-link the elements, if that makes sense.
That might be a solution for the out of control WLTKD. But then something would of course be done about the rest of the UA, I mean removing the permenent WLTKD would be a MASSIVE blow towards the later game power of the UA. And yes I understand that you probably figured that out by yourself, I just figured someone needed to mention it anyways.