I find it strange that the ruins cannot be marked for deconstruction.

You first have to claim them with the claim tool as the buildings belong to the enemy force.

The tool doesn't seem to work reliably with gun turrets sometimes so I disabled the mod leading to the described issue. Oversight by me.

I don't know why turrets cannot be claimed, maybe from far distance or remote-view you can try it. Maybe it is a game mechanic.

The claim-tool's data can be found in data.lua:

    select = {
      border_color = {1, 1, 1},
      mode = {"buildable-type", "not-same-force", "friend"},
      cursor_box_type = "train-visualization",
    },
    alt_select = {
      border_color = {1, 1, 1},
      mode = {"any-entity", "not-same-force", "friend"},
      cursor_box_type = "train-visualization",
    },

The claiming code can be found in lua/events.lua, search foron_player_selected_area` and you can find the "hook" function.

It may be limited to Fortress Ruins set or the base ruins set. I don't think the silly ruins set has any turrets.

Yes, some base ruins have turrets in them. The enemy force's name is AbandonedRuins:enemy BTW, not the vanilla enemy name.