I think the reason is simple. lists are ordered, dicts (prior to Python 3.6/3.7) and sets are not. So modifying a lists as you iterate may be not advised as best practise, but it leads to consistent, reproducible, and guaranteed behaviour.
You could use this, for example let’s say you wanted to split a list with an even number of elements in half and reverse the 2nd half:
>>> lst = [0,1,2,3]
>>> lst2 = [lst.pop() for _ in lst]
>>> lst, lst2
([0, 1], [3, 2])
Of course, there are much better and more intuitive ways to perform this operation, but the point is it works.
By contrast, the behaviour for dicts and sets is totally implementation specific since the iteration order may change depending on the hashing.
You get a RunTimeError with collections.OrderedDict, presumably for consistency with the dict behaviour. I don’t think any change in the dict behaviour is likely after Python 3.6 (where dicts are guaranteed to maintain insertion ordered) since it would break backward compatibility for no real use cases.
Note that collections.deque also raises a RuntimeError in this case, despite being ordered.