thresholds[size] = thresholds[size] + thresholds[ruin_sizes[i]]
needs to be i - 1 to add previous threshold to current instead of doubling current.

      if spawn_chance <= storage.spawn_chances[size] then
        if debug_log then log(string.format("[on_chunk_generated]: Trying to spawn ruin of size='%s' at event.surface='%s' ...", size, event.surface)) end
        try_ruin_spawn(size, min_distance, center, event.surface, event.tick)
      end

needs break before end . Currently when spawning small ruin it will also try to spawn all bigger sizes.

In clear_area(half_size, center, surface)
the loop
for _, entity in pairs(surface.find_entities_filtered({area = area, type = {"resource"}, invert = true})) do
handles entities that are sometimes invalid and sometimes deletes invalid entities. Every time you log invalid entity.name or entity.type it causes a crash.

Thank you for reporting this. I wasn't noticing the first two errors during game play.

For the last one, I posted such a crash here. So what do you suggest here? Skip every entity that has entity.valid == false? Can surface.find_entities_filtered() return an empty entity (nil) as well?

According to the documentation https://lua-api.factorio.com/latest/classes/LuaSurface.html#find_entities_filtered - it doesn't support a filter for valid entities. So I have to skip them in my code instead, if that's the proper fix.

EDIT: Filtering directly for valid = true or something isn't supported:
https://lua-api.factorio.com/latest/concepts/EntitySearchFilters.html

So my debug message crashes it?

Gee! I cannot tell Factorio to update it's GUI after a ruin set has been added to current-ruin-set's selection box. :-(

Okay, I can add lua/constants.lua which needs to be included and then get the proper "constant" from it. The mod realistic-ruins-updated will demonstrate it.

clear_area() is clearly deleting even invalid entities on purpose. What you need to do is make sure that you don't log entity.name and entity.type when entity is invalid. e.g:

  for _, entity in pairs(surface.find_entities_filtered({area = area, type = {"resource"}, invert = true})) do
    if debug_log then log(string.format("[clear_area]: entity.valid='%s'", entity.valid)) end
    if debug_log and entity.valid then log(string.format("[clear_area]: entity.type='%s',entity.name='%s'", entity.type, entity.name)) end
    if (entity.valid and entity.type ~= "tree") or math.random() < (half_size / 14) then
      if debug_log then
        if entity.valid then
          log(string.format("[clear_area]: Destroying entity.name='%s' ...", entity.name))
        else
          log("[clear_area]: Destroying invalid entity")
        end
      end
      entity.destroy({do_cliff_correction = true, raise_destroy = true})
    end
  end

Ah, it doesn't work all together when the entity is invalid. I wasn't noticing this error since it didn't happen so often here.

EDIT: And thank you for reporting this. 1.3.4 addresses this now.