Quote from Arkenor
Tower placement in v.5.52.002 seemed fine for me, though of course I was playing single-player, and something needed to be done to get it working for multiplayer.
However, v.5.52.003 seems to have taken to placing towers in some very inappropriate places.
I was getting this in .002 with vanilla biomes so it isn't new. With biome altering mods such as Biomes O'Plenty pretty much every tower I found was either in a cut out square hole in the ground or up on a base it generated like in yours. Biome generation mods also wreck havoc on village spawns to so I'd expect those mods to cause the problems however.