You could "just" crop by subtracting shapes manually every time, too. Rectangle crops are extremely common so it makes sense to have a tool for that even if it just generates the underlying concept(as with shape-to-path).

If I were approaching the problem fresh, though, I would look into the presentation of the modal functions as the root of the issue. The source of a lot of complexity in image editing software is confusion over layers, masks, groups, and selections - they have some conceptual overlap and can be applied modally(e.g. shape as rendering element OR mask OR selection). If the UI buries the difference it just adds to the confusion.