Water is not at a consistent level across Lake Michigan, with many swells, bulges, and waves.
Granted, but in your world the lake is flat, right? Yes, there are waves and bulges but the base level is flat. Unless there's a storm the waves and bulges aren't going to be that big
If your eye level is higher than the highest wave then less of the building than the wave height will be occluded, you're looking over the top of the waves.
Even if the wave height is at your eye level only the height of the wave will be occluded:
It's only if your eye height is
lower than the wave height that more of the building than the wave height will be occluded. So unless your eye level is very low or there are very big waves or swells, that is not a valid explanation.
Do you reject it as an explanation for why any part of a building is occluded and accept it as an explanation for the fact more of a tall building is seen than is mathematically possible given the dimensions of the supposed spherical earth?
I reject waves for the reason I've given above. Atmospheric effects are more plausible and the photos show different results which does imply differing conditions which can cause different observations.
But I've yet to see any examples of the whole building being seen. You'd think if the earth were flat then
sometimes you'd see all of it on a particularly clear day. From that distance the angle the light from the top and bottom of the building is so similar that I'm sceptical that the top of the building would be so clear and the bottom completely hidden.
There's a pretty sharp horizon line below the tops of the buildings. That tells me that something is blocking the rest of the building. In the globe earth model the something is the curve of the earth.