The <wp-inner-blocks> wrapper being added implicitly on the frontend is something block authors might not expect. It's not added in the editor right now, so anything relying on the DOM tree needs to handle two versions. Most notably this is styles with relationship selectors.

For example, Sensei's Flashcard block uses a structure where the first and second child blocks are considered the front and back of the card, respectively:

&--flipped-front > *:nth-child(1),
&--flipped-back > *:nth-child(2) { ... }

This is likely an edge case and can be worked around, but making it consistent across editor and frontend could improve the developer experience.