Strongholds and trial chambers can intersect.

Seed: -1316865467785382608
Coordinates: 9885 -19 6186

The easiest fix would be to make trial chambers fail to generate within 400 blocks or so of a stronghold origin. Ultimately, two solutions to this kind of problem should be considered: the conversion of older structures to jigsaw generation and the implementation of a data-driven hierarchy of underground structures. For the latter, I suggest grouping structures into tiers; structures higher in a tier inhibit others in that tier from generating nearby while also completely overwriting structures in lower tiers. (If implemented correctly, #features_cannot_replace could probably be deprecated.) For the vanilla overworld this would probably be:

• Tier 1
  • Stronghold
  • Ancient city
  • Trial chamber
• Tier 2
  • Mineshaft
• Tier 3
  • Monster room/dungeon (should probably also have additional logic to avoid generating inside other structures to prevent weird interactions like MC-265371)
  • Geode

This suggestion is WIP, a proper fix should also account for igloos, monuments and the like.