Well, there are plenty of papers using a cross-nested logit would do.
Here is a recent model that we have developed:
The intuition is simple. The reason why you need a two-level nested logit is because there is no partition of the choice set that captures the correlation structure that you have in mind. Some of the alternatives (or all of them) potentially belong
to more than one nest. And the nested logit model is therefore not applicable. But this is exactly the purpose of the cross-nested logit model. It does not rely on a partition. Alternatives can belong to more than one nest. In addition, the cross-nested logit
is more flexible than the two-level nested logit model.