It's not just you, I'm having the same problem!

Does the example make more sense intuitively if it is worded as: "Wherever the judges are independent, there will be a good legal system"?

'Where' belongs in Group 1 for the same reason 'when' does. Without the word 'only' in front of it, 'when' means: at any/all times. Similarly, when 'where' appears without the word 'only' in front of it, it means: in any/all places. So if the example statement is true, then we know that wherever you look, if you find independent judges, there will be a good legal system there.

If it helps, think of 'where' and 'when' as equivalent to 'wherever' and 'whenever.' And if you actually see the words 'wherever' or 'whenever,' those definitely go in Group 1.