I dislike Worley's Caves, so I took it out to see what a world would look like without it. I was surprised to find that the building damage in the Lost Cities was much reduced. Some time ago I had also been experimenting with the 'nodamage' attribute for Lost Cities, and was disappointed that it seemed to have no effect. It tried it just now, and with Worley's Caves off all the buildings were pristine.

So, as you've obviously guessed, it appears that Worley's Caves generates caves inside of all the buildings of the Lost Cities as well. I'm guessing this is because the max height in the Worley's Caves config is set to 128, so it hits the vast majority of the buildings.

I don't know if this is something worth fixing, but I wanted to bring it to your attention.

That's an interesting finding. My concern with changing it is that it would also affect the nether, whose roof is at y=128. The overworld can technically generate features up to Y=255 as well, so it would affect generations in mountains and hills if we were to reduce it to something like minecraft's "sea level".

For what it's worth, I was digging into the Worley's Caves source trying to find out what the 'allowReplaceMoreBlock' config option did (to see if it could help). The source has since been modified for 1.14-1.16 and the option is gone, but there is a comment in the source explicitly exempting the Nether and the End from Worley Cave generation. This jibes with my gut feeling that the Nether and the End were vanilla gen. (Very scientific, I know.)

So that scientific gut feeling is that changing the Max Y would affect the Overworld and possibly the Moon. Still might not be worth it, but something to consider.